Re: [gmx-users] Is there still interest in rigid-body simulation?

[ms]

On 27/03/11 23:02, Adam Herbst wrote:

Hi all,
I have seen a few posts on gmx-users indicating a desire to treat
certain atom groups as rigid bodies in MD simulations.  I just started
implementing this, and so far I have it working for translational forces
(not rotation, though this should be simple to add), even when the group
is split over multiple processors.  At the moment I have the rigid body
groups specified as freeze groups in the mdp file, but there could be a
separate option.  Would anyone else find this useful?  The problem is
that: (a) I am modifying GROMACS 4.5.1, so I am some months out of date,
and (b) my code is probably not to spec.  If it is worthwhile, I can
restart from 4.5.4 (the code modifications are quite small) and make an
effort to conform to coding standard.  Best,

Adam Herbst



I would love that!!

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Re: [gmx-users] adsorption

[ms]

On 27/12/12 16:29, vahid garshasbi wrote:

I run my simulation, now i want to analysis my data. i simulate ion
adsorption on CNT and i want to determine adsorption values in
deffrent concentrations of ion and then plot adsorpttion curve. what
shod i do?


Ask your advisor.



thanks, vahid




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[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

[ms]

Hi,

I am trying to prepare a simple system for tests with CUDA. My guinea 
pig is the lysozyme system from this tutorial: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html


but I prepared it using the AMBER99sb-ildn force field and the SPCE 
water model.


After extensive minimization steps, I started a (CPU) very short test 
run (3 ns) to check if everything was ok before beginning to deal with CUDA.


However I found that there is a strong drift in energy and temperature:

>g_energy_d output:

 Opened 1AKI_production_GPU.edr as double precision energy file

 Select the terms you want from the following list by
 selecting either (part of) the name or the number or a combination.
 End your selection with an empty line or a zero.
 ---
   1  Bond 2  Angle3  Proper-Dih.  4 
Improper-Dih.
   5  LJ-146  Coulomb-14   7  LJ-(SR)  8 
Coulomb-(SR)
   9  Coul.-recip.10  Potential   11  Kinetic-En. 12 
Total- Energy
  13  Temperature 14  Pressure15  Box-X   16 
Box-Y
  17  Box-Z   18  Volume  19  Density 20  pV 

  21  Enthalpy22  Vir-XX  23  Vir-XY  24 
Vir-XZ
  25  Vir-YX  26  Vir-YY  27  Vir-YZ  28 
Vir-ZX
  29  Vir-ZY  30  Vir-ZZ  31  Pres-XX 32 
Pres-XY
  33  Pres-XZ 34  Pres-YX 35  Pres-YY 36 
Pres-YZ
  37  Pres-ZX 38  Pres-ZY 39  Pres-ZZ 40 
#Surf*SurfTen
  41  Box-Vel-XX  42  Box-Vel-YY  43  Box-Vel-ZZ  44  Mu-X 

  45  Mu-Y46  Mu-Z 

  47  Coul-SR:Protein-Protein 48  LJ-SR:Protein-Protein 

  49  Coul-14:Protein-Protein 50  LJ-14:Protein-Protein 

  51  Coul-SR:Protein-non-Protein 52  LJ-SR:Protein-non-Protein 

  53  Coul-14:Protein-non-Protein 54  LJ-14:Protein-non-Protein 

  55  Coul-SR:non-Protein-non-Protein 56 
LJ-SR:non-Protein-non-Protein
  57  Coul-14:non-Protein-non-Protein 58 
LJ-14:non-Protein-non-Protein

  59  T-System

10
11
12
13
14

 Last energy frame read 3 time 5000.000

 Statistics over 301 steps [ 2000. through 5000. ps ], 5 
data sets

 All statistics are over 151 points

 Energy  Average   Err.Est.   RMSD  Tot-Drift

---
 Potential   -529618   15003004.68   -10322.5 
 (kJ/mol)
 Kinetic En. 86141.8610 1295.7   -4294.67 
(kJ/mol)
 Total Energy-443476   21004220.26   -14617.1 
(kJ/mol)

 Temperature  292.492.14.39949   -14.5823   (K)
 Pressure1.02119 0.0046133.601 -0.0134421 
(bar)


 You may want to use the -driftcorr flag in order to correct
 for spurious drift in the graphs. Note that this is not
 a substitute for proper equilibration and sampling!

 WARNING: nmol = 1, this may not be what you want.

Temperature dependent fluctuation properties at T = 292.49.


The MDP is:

>production_GPU.mdp

; PREPROCESSING OPTIONS
title   = production run 1 for GPU usage
include =
define  =
; RUN CONTROL PARAMETERS
integrator		= md		; for GPUs: "Option md is accepted but keep in mind 
that the actual algorithm is not leap-frog."


tinit   = 2000
dt  = 0.001 ; 1 fs
nsteps  = 300   ; 3 ns
init_step   = 0
; CENTER OF MASS MOTION REMOVAL
nstcomm = 1
comm_mode   = linear
comm_grps   = protein non-protein
; OUTPUT CONTROL
nstxout			= 2000		; Doubled these because disk output is a strong 
bottleneck apparently


nstvout = 2000
nstfout = 0
nstlog  = 100
nstenergy   = 100
nstxtcout   = 100
nstcalcenergy   = -1
xtcprecision= 1000
energygrps  = protein non-protein
; NEIGHBOR SEARCHING PARAMETERS
nstlist = 2.
ns_type = grid
pbc = xyz
rlist   = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME   ; this is OK for GPUs
rcoulomb_switch = 0.
rcoulomb= 1.0
epsilon_r   = 1
vdwtype = cut-off
rvdw-switch = 0.
rvdw= 1.0
DispCorr= no
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-05
epsilon_surface = 0
optimize_fft= no
; TEMPERATURE COUPLING
tcoupl			= andersen	; All values of this are equivalent to "andersen" in 
GPU mode

tc_grps  

[gmx-users] Re: Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

[ms]

Looking deeper, it seems most of the energy loss is concentrated in the 
SR Coulomb interactions:


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Bond2771.28 1792.5698   -120.382 
(kJ/mol)
Angle3796.4 25106.584   -169.737 
(kJ/mol)
Proper Dih. 5106.24 1054.0963   -66.3269 
(kJ/mol)
Improper Dih.   261.4211.721.1174   -11.8454 
(kJ/mol)
LJ-14   1865.58   0.5936.7259   -2.92646 
(kJ/mol)
Coulomb-1416174 14  118.8   -58.9593 
(kJ/mol)
LJ (SR) 94061.95601333.143958.04 
(kJ/mol)
Coulomb (SR)-578731   19004045.78   -13704.5 
(kJ/mol)
Coul. recip.   -74923.8 2381.0255   -145.854 
(kJ/mol)
Potential   -529618   15003004.68   -10322.5 
(kJ/mol)
Kinetic En. 86141.8610 1295.7   -4294.67 
(kJ/mol)
Total Energy-443476   21004220.26   -14617.1 
(kJ/mol)

Temperature  292.492.14.39949   -14.5823  (K)
Pressure1.02119 0.0046133.601 -0.0134421  (bar)
Volume  343.801   0.32   0.955516-2.2844  (nm^3)
Density 1012.34   0.942.813496.72636 
(kg/m^3)




Also, the drift is almost perfectly linear (apart from the noise).


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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

[ms]

On 13/06/12 16:36, Justin A. Lemkul wrote:

Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some instabilities.


This is interesting -I have to ask the guys who devised the group's 
standard procedure :)



mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s
1AKI_production_GPU.tpr
-g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o
1AKI_production_GPU.trr
-g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr



As an aside, proper use of -deffnm (not -deffn) saves you all of this
typing :)

mpirun -np 8 mdrun_d -v -deffnm 1AKI_production_GPU

That's all you need.


 that's why -deffn it didn't work! silly me. Thanks!


I am using Gromacs 4.5.5 compiled in double precision.

I am very rusty with Gromacs, since I last dealt molecular dynamics
more than 1
year ago :) , so probably I am missing something obvious. Any hint on
where
should I look for to solve the problem? (Also, advice on if the .mdp
is indeed
correct for CUDA simulations are welcome)



I see the same whenever I run on GPU, but my systems are always implicit
solvent. Do you get reasonable performance with an explicit solvent PME
system on GPU? I thought that was supposed to be really slow.

>

Do you observe similar effects on CPU? My tests have always indicated
that equivalent systems on CPU are far more stable (energetically and
structurally) than on GPU. I have never had any real luck on GPU. I get
great performance, and then crashes ;)


Sorry, perhaps I wasn't clear. This was on normal CPUs! I was trying to 
get the system working on CPU and to see how it behaved before diving in 
the GPU misty sea...


thanks,
Massimo

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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

[ms]

On 13/06/12 16:59, Justin A. Lemkul wrote:



On 6/13/12 10:48 AM, ms wrote:

On 13/06/12 16:36, Justin A. Lemkul wrote:

Here, you're not preserving any of the previous state information.
You're picking up from 2 ns, but not passing a .cpt file to grompp - the
previous state is lost. Is that what you want? In conjunction with
"gen_vel = no" I suspect you could see some instabilities.


This is interesting -I have to ask the guys who devised the group's
standard
procedure :)


mpirun -np 8 mdrun_d -v -deffn 1AKI_production_GPU -s
1AKI_production_GPU.tpr
-g 1AKI_production_GPU.log -c 1AKI_production_GPU.gro -o
1AKI_production_GPU.trr
-g 1AKI_production_GPU.log -e 1AKI_production_GPU.edr



As an aside, proper use of -deffnm (not -deffn) saves you all of this
typing :)

mpirun -np 8 mdrun_d -v -deffnm 1AKI_production_GPU

That's all you need.


 that's why -deffn it didn't work! silly me. Thanks!


I am using Gromacs 4.5.5 compiled in double precision.

I am very rusty with Gromacs, since I last dealt molecular dynamics
more than 1
year ago :) , so probably I am missing something obvious. Any hint on
where
should I look for to solve the problem? (Also, advice on if the .mdp
is indeed
correct for CUDA simulations are welcome)



I see the same whenever I run on GPU, but my systems are always implicit
solvent. Do you get reasonable performance with an explicit solvent PME
system on GPU? I thought that was supposed to be really slow.

>

Do you observe similar effects on CPU? My tests have always indicated
that equivalent systems on CPU are far more stable (energetically and
structurally) than on GPU. I have never had any real luck on GPU. I get
great performance, and then crashes ;)


Sorry, perhaps I wasn't clear. This was on normal CPUs! I was trying
to get the
system working on CPU and to see how it behaved before diving in the
GPU misty
sea...



Ah, sorry - with everything being named "GPU" it threw me off. I guess I
should have known based on the energy terms. When running on GPU, very
little information is printed (something I've complained about before) -
you only get Potential, Kinetic, Total, Temperature, and anything
related to constraints. I think it's due to limitations in OpenMM, not
Gromacs (something that should be improved in upcoming versions).

A few things to look at based on the .mdp file:

1. No constraints? Even with a 1-fs timestep, you probably need to be
constraining all least the h-bonds.


Ok. We usually don't constrain with 1-fs timestep, and since the gmx 
website said that most restrains were unsupported, I didn't feel like 
adding them. Will ask about this here.



2. nstlist set to 2 is not going to give wrong results, but it's
incredibly time-consuming to do neighbor searching that often. A value
of 5 or 10 is probably more appropriate.


I have to ask why we use this value as default, and thanks for the tip 
-however this seems not relevant now :)



3. COM removal of multiple groups can lead to bad energy conservation.


OK, good to know.


4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the 4.6 development branch). Your comment regarding GPU is fine, but I
would think grompp would complain.


I am unsure of what do you mean. On the gmx website it reads:
"Temperature control: Supported only with the sd/sd1, bd, 
md/md-vv/md-vv-avek integrators. OpenMM implements only the Andersen 
thermostat. All values for tcoupl are thus accepted and equivalent to 
andersen. Multiple temperature coupling groups are not supported, only 
tc-grps=System will work."


So it seems that *every* choice of mine means "andersen" in that 
context. Am I wrong?



5. Why not use dispersion correction?


True, why not? :)
Will give it a shot.


thanks!
m.

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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

[ms]

Ok, I tried some of your suggestions and the Coulomb-SR energies still 
fall down very quickly.


I wonder if:

On 13/06/12 16:59, Justin A. Lemkul wrote:

4. What happens when you use the Andersen thermostat? That's not
implemented yet for CPU calculations (though it was recently pushed into
the 4.6 development branch). Your comment regarding GPU is fine, but I
would think grompp would complain.


maybe mdrun *tries* to use Andersen but since it's not fully implemented 
for CPUs it makes odd artefacts?



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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]

[ms]

Ok, I am using v-rescale now and the major artefacts seem to be gone, at 
least on the very short term (2-3 ns).


It seems grompp should warn that andersen is not a good choice if you're 
using CPUs :)


Thanks!
M.

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Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]

[ms]

On 15/06/12 13:02, Justin A. Lemkul wrote:


In the existing code for version 4.5.5, it seems the "Andersen" keyword
is accepted but there is no mention of its use in update.c or
coupling.c, suggesting to me that it's a ghost parameter that does
nothing. There should be some indication in the .log file that there
might be a problem and/or problems with the temperature should be apparent.


Apparently, logs said nothing. Do you want to give it a read if you can 
find something odd?



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Re: [gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules

[ms]

On 27/06/12 05:20, Surya Prakash Tiwari wrote:

Dear Gromacs users,

I am having a very strange problem with "Nose Hoover thermostat with
Parrinello-Rahman barostat" NPT simulations for a system of an ion of
charge +2 in flexible water molecules. Flexible water is taken from J.
Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877.
The ion is [UO2]2+ with charge on U=2.5 and each O has -0.25.

Atoms very soon get frozen after the simulation starts and they remain
frozen, they do not move at all. Only simulation box oscillates, which
causes atoms to oscillate little bit but they do not move at all.


To me it looks like a case of this artefact:

http://en.wikipedia.org/wiki/Flying_ice_cube

but I don't know exactly what is causing it in your system. Perhaps the 
article can help you triage...


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Re: [gmx-users] Structure optimization failure

[ms]

On 29/06/12 19:59, Justin A. Lemkul wrote:


Wouldn't it be nice to create a table of "standard settings" for each
forcefield
in the gmx documentation (with lit references of course)?



Well, anyone is welcome to submit anything they feel would be useful... ;)

I have considered this in the past, but have rejected the thought every
time it comes to mind. It would be nice if there was a central
repository of such parameters, but then likely a simulation becomes "do
this, not that" with no required thought from the end user.
If you make
simulations a black box, everyone expects them to automatically work
without fail.


Which should be what it has to be in an ideal world :)

Apart from that, it wouldn't mean to make them a black box -quite the 
opposite. Giving parameters *with* an explanation of them, literature 
quotes etc. would give tremendous insight to lots of people that often 
just use "the lab's standard .mdp" and tweak it.


This doesn't mean everyone would expect them to work without fail, it 
would give however a good starting point.



The other objection I have always had is the continual improvement of
the field. If Gromacs puts out an "official" or "standard" list of what
to do, it is always subject to change and then becomes incumbent upon a
Gromacs contributor to verify its accuracy frequently. My personal fear
is that this becomes an untenable task.


Isn't that however the point of a scientific community -sharing and 
updating knowledge? We use to rely on papers, but that's far more 
inefficient than having a centralized repo where we can share and 
discuss informations.



Then in the case of an error,
someone's whole Ph.D. could go out the window...


I suspect without this even more Ph.D's get wasted -because they don't 
really know what to do and just crank things together without really 
getting it. Not all of us have received proper education on MD (I didn't 
for example -I had to learn everything by myself and I am a total newbie 
even after a couple years) I mean, at least it gives a good starting 
point for people.



In the end, I think it's always safe to ask the user to do a bit of
legwork to understand the force field he or she wishes to use. The
knowledge gained from an hour of reading will save a lot of potential
headaches.


Sure, and in fact I would expect such a page etc. to *start* with 
literature references and even directly quoting papers when explaining 
why certain params and not others.



I would reject any attempt to include such information in the manual
(lest its settings become "official"), but if someone wants to put up a
wiki page on the website with clear warnings and disclaimers, they are
welcome to do so.


I am probably the least qualified person to do so, but I'd enjoy to 
collaborate.


m.


Just my $0.02.

-Justin




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[gmx-users] Compilation of Gromacs 4.5.5 with GPU support: libxml and CUDA toolkit problems

[ms]

Hi,

I am trying to compile Gromacs 4.5.5 with GPU support on Linux. I have 
performed the following steps:


export OPENMM_ROOT_DIR=/home//gromacs/OpenMM2.0-Linux64/
mkdir build-gpu
mkdir exec-gpu
cd build-gpu
cmake ../  -DGMX_OPENMM=ON -DFFTW3F_INCLUDE_DIR=/usr/lib/include 
-DFFTW3F_LIBRARIES=/usr/lib/libfftw3f.a 
-DCMAKE_INSTALL_PREFIX=../exec-gpu -DGMX_X11=OFF 
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_DEFAULT_SUFFIX=OFF 
-DGMX_BINARY_SUFFIX="_gpu" -DGMX_LIBS_SUFFIX="_gpu" -DGMX_DOUBLE=OFF 
-DGMX_MPI=OFF -DLIBXML_INCLUDE_DIR=/usr/lib


but it fails with:

-- Using manually set binary suffix: "_gpu"
-- Using manually set library suffix: "_gpu"
-- checking for module 'libxml-2.0'
--   package 'libxml-2.0' not found
-- Could NOT find LibXml2 (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
CMake Error at cmake/FindCUDA.cmake:465 (message):
  Specify CUDA_TOOLKIT_ROOT_DIR
Call Stack (most recent call first):
  CMakeLists.txt:434 (find_package)

For libxml2: I have libxml2.so.2 in /usr/lib
I tried the following:

- export LIBXML2_INCLUDE_DIR=/usr/lib
- export LIBXML2_LIBRARIES=/usr/lib/libxml2.so.2
- adding -DLIBXML2_INCLUDE_DIR=/usr/lib

but it continues to fail.

About the CUDA_TOOLKIT_ROOT_DIR, I don't know where to find it honestly.

Any hint on how to find a solution?

Thanks a lot,
Massimo

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Re: [gmx-users] Re: v-rescale

[ms]

On 20/09/12 01:35, Peter C. Lai wrote:

then switching to nose-hoover for production
runs (as nose-hoover chains result in the correct canonical distribution)?


I was under the impression that v-rescale resulted in the correct 
canonical distribution as well. Is this incorrect?



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Re: [gmx-users] g_energy menu choices inconsistent?

[ms]

On 02/10/12 11:53, Justin Lemkul wrote:


Note that you can always select by name rather than number, i.e.:

echo Temperature | g_energy -f ener.edr


Didn't know that, this really saves me a lot of trouble! Thanks Justin!

m.


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Re: [gmx-users] WHAM

[ms]

Hi Justin,

On 17/09/10 11:51, Justin A. Lemkul wrote:

Also in section 5.3 is the procedure for how to use REMD data, but I
don't think it will ever accomplish what you want. The input into WHAM
would be energies, not RMSD vs. R(g), as you initially stated as your
goal. You can easily build free energy surfaces of RMSD vs. R(g) using
g_sham, however.


I am wondering: Is there an already-done way, for a REMD set of 
trajectories, to allow g_sham to extract the surface only from a given 
temperature, from all replicas?


thanks!

m.
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Re: [gmx-users] WHAM

[ms]

On 18/09/10 18:32, Justin A. Lemkul wrote:

Hi Justin,

On 17/09/10 11:51, Justin A. Lemkul wrote:

Also in section 5.3 is the procedure for how to use REMD data, but I
don't think it will ever accomplish what you want. The input into WHAM
would be energies, not RMSD vs. R(g), as you initially stated as your
goal. You can easily build free energy surfaces of RMSD vs. R(g) using
g_sham, however.


I am wondering: Is there an already-done way, for a REMD set of
trajectories, to allow g_sham to extract the surface only from a given
temperature, from all replicas?



There's nothing automated that I'm aware of. The trajectories should be
ensemble-continuous, so you should be able to conduct whatever analysis
you want on any particular temperature. You'll have to construct the
.xvg input into g_sham though, such that the data represented are in two
columns, so unfortunately, in the case of RMSD vs. R(g), you have to do
additional scripting.


Ok, very clear, thank you!!

m.
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Re: [gmx-users] Tables with forcefield

[ms]

On 21/09/10 20:45, Sai Pooja wrote:

I wanted to change the interactions between the Protein and Solvent so I
tried using tables with the potential function scaled by a constant value. I
wanted to use this in combination with forcefield parameters (charmm). I
changed the combination rule in the forcefield.itp file from '2' to '1'
since tables use C6 and C12 values. To test the system I started with
default tables.

When I run grompp, it generates the .tpr file successfully but in the md
simulation using mdrun, settle does not converge. It does not converge for 1
water molecule.

If I go back to the combination rule '2' in the forcefield.itp file, I get a
warning that using combination rule 2 with tables may generate error.

With combination rule '2' and cutoff for both vanderwaals and coulombtype, i
face no problem.


I use combination rule 1; but I also define all tabulated interactions 
for all possible *pairs* under the [ nonbond_params ] section, so the 
combination rule actually doesn't matter much.



Does this mean that one cannot use tables with forcefield parameters?


I am not sure of understanding with question -can you clarify?

Massimo

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Re: [gmx-users] Tables with forcefield

[ms]

Hi,

Clarification: I may not be able to help you directly but I can suggest 
you which information you should perhaps give us to enable people more 
knowledgeable than me to help.


On 24/09/10 17:33, Sai Pooja wrote:

I use combination rule 1; but I also define all tabulated interactions for
all possible *pairs* under the [ nonbond_params ] section, so the
combination rule actually doesn't matter much.



Are you suggesting that I can change the combination rule in the
forcefield.itp file but I must also supply a table for pairs using -tablep
option for this to work?


I am not "suggesting": I am only saying what I am doing :)


Does this mean that one cannot use tables with forcefield parameters?






Clarification: I want to use forcefield parameters with user defined tables
i.e. I want to use sigma and epsilon values generated by pdb2gmx along
with a user-defined modified potential energy function using tables.


This is absolutely doable -I do it everyday, in fact. So, don't despair. :)

Now, it seems that you talked about a problem with convergence of the 
SETTLE algorithm. I know little about it, but, couldn't it simply be 
that your tables are "wrong" (that is, they don't play well with 
algorithms?) What is their shape, actually, and on which 
atomtypes/groups are you applying your table? What is the forcefield you 
are using along with the table?


M.
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[gmx-users] Force field definitions in 4.0 and 4.5

[ms]

Dear users,

I am currently using GROMACS 4.0.7 with a custom force field I developed 
(coarse-grained model I am developing). I want to jump to 4.5 , but I 
wonder if something in the syntax of force fields has changed from 4.0.x 
to 4.5 :just to know in advance if I have to change the files or if I 
can just copy-and-paste them :)


thanks!
Massimo
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Re: [gmx-users] Force field definitions in 4.0 and 4.5

[ms]

On 11/10/10 15:45, Justin A. Lemkul wrote:

I am currently using GROMACS 4.0.7 with a custom force field I
developed (coarse-grained model I am developing). I want to jump to
4.5 , but I wonder if something in the syntax of force fields has
changed from 4.0.x to 4.5 :just to know in advance if I have to change
the files or if I can just copy-and-paste them :)


You should be able to rename the files to fit the new directory scheme
and put all of them together in a .ff subdirectory. I've done that
with a few custom force fields and it seems to work just fine.


Cool, thanks! I'll see about the new directory scheme.

Massimo
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[gmx-users] Compiling with ICC: advantages and -if yes- a suitable protocol? (it seems I can't)

[ms]

Dear gmx users,

I have heard (read: read on random blogs here and there) that on Intel 
compiling GROMACS with icc instead of gcc can bring up to 50% 
performance improvement.


Since I always used gcc compiled GROMACS, I'd like to know:
- Is this true?
- If yes, can anybody help me in doing so? I tried but I cannot find a 
reasonable protocol online and setting LDFLAGS gives me quite an 
headache : my last configure dies this way:


$ export CC=/opt/intel/Compiler/11.0/081/bin/intel64/icc
$ export LDFLAGS="-L$SOFT/lib -L/opt/intel/Compiler/11.0/081/lib/intel64 
-lguide -lpthread"

$ ./configure --with-fft=fftw3 --program-suffix=_icc --enable-mpi

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for C compiler default output file name... a.out
checking whether the C compiler works... configure: error: cannot run C 
compiled programs.


where config.log says, in the relevant section:

configure:3441: /opt/intel/Compiler/11.0/081/bin/intel64/icc 
-I/home/ms872/software/include -L/home/ms872/software/lib 
-L/opt/intel/Compiler/11.0/081/lib/in

tel64 -lguide -lpthread conftest.c  >&5
configure:3444: $? = 0
configure:3482: result: a.out
configure:3499: checking whether the C compiler works
configure:3509: ./a.out
./a.out: error while loading shared libraries: libguide.so: cannot open 
shared object file: No such file or directory

configure:3512: $? = 127
configure:3521: error: cannot run C compiled programs.

but if I look for this library:
$ locate libguide.so
/opt/intel/Compiler/11.0/081/lib/intel64/libguide.so

...that seems therefore to be in the LDFLAGS!

Note that I am trying to compile 4.0.7 and not 4.5.1 (because I then 
need to apply 3rd-party patches that do not apply to 4.5.1 yet -but 
before thinking of that, I want to get the compilation right, so now 
it's vanilla gromacs)


It's clear that I am no C hacker, so thanks to everyone that can help me.

Massimo
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Re: [gmx-users] Compiling with ICC: advantages and -if yes- a suitable protocol? (it seems I can't)

[ms]

On 12/10/10 00:33, Mark Abraham wrote:

I have heard (read: read on random blogs here and there) that on
Intel compiling GROMACS with icc instead of gcc can bring up to
50% performance improvement.


If you are referring to this post 
(http://kent-vandervelden.blogspot.com/2010/08/optimization-of-gromacs-407.html)
 then his comparison is based on use of FFTPACK, and is at best misleading. 
I've posted a follow-up comment that is awaiting approval. He didn't cite 
relative performance for gcc+mkl, for starters.


Among others, yes :)


GROMACS performance is dependent on
a) non-bonded kernels (which are coded in assembler for the large majority of 
platforms for which icc exists, and so compiler version is largely irrelevant)


I use mostly tabulated functions for the model I'm developing...


b) FFT performance (only for PME, and gcc+FFTW3 is only a few percent behind 
icc+MKL in my tests)


OK, good.


c) a whole pile of MD algorithmic effects (but time spent in these is 
negligible compared with those above)
You can see this immediately in the timing breakdown reported at the end of the 
mdrun .log file.


Yep, I know. Thanks!


Since I always used gcc compiled GROMACS, I'd like to know:
- Is this true?


No.


Great. So I can stop bothering and keep my happy gcc :)

Thanks!
Massimo
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Re: [gmx-users] Please guide me

[ms]

On 14/10/10 08:51, mohsen ramezanpour wrote:

Dear All

I am running a seamulated anneaking + MD in my cluster.
I had done it for 2 times.
but my results are not as i expect.
I have attached my md.mdp file for you,I don't know which part of it is
wrong.
what i like to result is to change tempreture from 420 in 0 ps to 450 in 20
ps and then gradually lowering tempreture to 300 in 850 ps.and
this fix tempreture by the end of simulation.
but all of my result who I extract T-plot of them show me just untill 2 ps.
then it is incomplete.


Are you sure your simulation doesn't crash?


Really I don't know what I must to do.
Please let me know my wrong.
Please guid me and edit my md.mdp file for this foal if it is possivle.
I am waiting for your reply
Thanks oin advance for your reply

Sincerely
Mohsen




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Re: [gmx-users] Questions about REMD calculations

[ms]

On 14/10/10 17:32, XAvier Periole wrote:


Then I am not a fan of implicit solvents so I'll pass on that, then for the
coarse grained FF the OPEP FF seem to be fine for your application.
You can also look at the ones from Deserno's group (bereau-2009) and
from Feig's group (primo: gopal-2010). I am no sure how the one of voth
is transferable ... the others are :))


Is OPEP available as a Gromacs FF? I suspect that it is not trivial to 
port to Gromacs, it includes explicit directional (angle-dependent) 
hydrogen bond interactions, for example, which to my knowledge Gromacs 
does not support.


I'd like if it was available though.

m.
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[gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

Hi,

It's a bit long but bear with me if you can. I'm getting quite mad with 
this. Thanks :)


Now. I am using Gromacs (4.0.7 currently) to create a custom 
coarse-grained, no-solvent MD peptide model -one that contains the 
backbone but has only C-alphas, no side chains.


To enforce chirality in such a toy, I thought that a simple (naive?) but 
functional idea could be that of enforcing a not-too-hard and 
wide-bottomed dihedral restrain on the phi angle, like that:


[ dihedral_restraints ]
; ai   ajakal  type  label  phi  dphi  kfac  power
; phi C'(n-1) - N - CA - C'
  3 5   7   8   11  -90 752  1

so that the system is free to move in a large phi-angle space without 
problems, but cannot go in the forbidden, symmetrical glycine-like 
space. In testing, I set the force constant small (10) so that the 
chain, even if with some difficulty, should be able to bend and move by 
spending some energy in the "forbidden" zones, if needed to achieve 
structure, etc.


Now, the point is that *when* it works, it works quite well. But 
sometimes -with "sometimes" being from 0% to 90% of times, depending on 
details of what I am simulating- it totally doesn't. That is: sometimes, 
starting from an extended structure, the chain simply freezes. It is not 
static: it wiggles a bit here and there, but it stays mostly extended. 
Energies plots (g_energy output xvg's) are on average flat: that is, 
they show the right noise for all components, but no structure: nothing 
happens, for as much as 50 ns.


Sometimes instead it works, and then you see that everything works 
alright; the peptide structures, potential energy goes down and down, 
etc.etc.


There are no differences in minimization energies etc. from a simulation 
that freezes and one that works. Moving the restraint center doesn't 
help much. I *know* it's the restraints because if I keep everything the 
same but I lower the force constant or remove restraints altogether, the 
freezing bug happens no more -but then I have little or no more 
chirality, of course. I have the following further facts:
- It tends to happen more often for longer chains: 10 or 20-residue long 
chains work often OK, but a 40-long chain is difficult to get "right".
- It *never* happens, to my knowledge, if I put more than 1 chain to 
cluster in the box.
- The Ramachandran plot of the extended frozen thing is "right", meaning 
that it populates a reasonable (mostly beta) angle space. During 
trajectory angles move quite a bit but stay in the right (top-left) zone 
of the plot.
- "Good"-behaving simulation often start with a short "frozen" stretch: 
then the dihedral restraint energy suddenly jumps to some above noise 
positive value, to accomodate some bending I guess, and all goes 
downhill from there.
- In frozen simulations, there's almost no LJ energy: the chain does not 
self-interact.


All of this, added to the apparent "randomness" of the pathology, makes 
me think that the chain simply is stuck in a situation where it has a 
too high barrier to properly bend -a barrier which is not a "soft" one 
as the harmonic potential of the restrain would make me think. This 
would explain why putting more peptides and letting them bind together 
avoids the problem: the potential energy of binding compensates for the 
bending when you have more than one thing; but sometimes a single chain 
cannot find itself to interact with, because it should bend correctly to 
do so.


And then, I read on the Gromacs website *this*
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
" 2. The manual is a bit unclear about whether this type of dihedral 
restraint is stable for use near 180 degrees. Chris Neale has found that 
everything appears to behave normally and as expected over the entire 
range of dihedral angles including 180 degrees. However, one must avoid 
the situation in which the actual dihedral is close to 180deg away from 
the restrained dihedral."


And I know that somehow the potential is discontinuous and/or anyway not 
intended to be well-behaved everywhere:

http://www.mail-archive.com/gmx-users@gromacs.org/msg12353.html

"> On Tue, Feb 26, 2008 at 11:37 AM, David Mobley <[EMAIL PROTECTED]> wrote:
> >  The other way of putting what Mark said is that phi is only 
meaningful on some range (-pi to pi, or 0 to 2pi, depending on how you 
define it)

> >  and so what you require is that the potential be harmonic for the
> >  region in which phi is meaningful. You don't care what happens 
outside that. Or, in this case, you handle the issue by mapping phi 
values  outside the allowed range back into that allowed range."


(I don't get what does it mean to "map back" phi values, by the way).

I am no MD expert, so maybe my hypothesis is totally off, but I am 
reasonably sure that either I do not understand correctly how dihedral 
restraints work, or I am suffering by the discontinuity of the way the 
potential is implemented (Or both).

Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

On 18/10/10 03:30, Mark Abraham wrote:

To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:

[ dihedral_restraints ]
; ai   ajak
al  type  label  phi  dphi  kfac  power
; phi C'(n-1) - N - CA - C'
   3
5   7   8   11  -90 752  1


Try mdrun -debug on a short run. What does it have to say about the parameter 
values for this dihedral restraint? Likewise gmxdump -s on the .tpr (though you 
will have to search around for F_DIHRES among other things, probably).



I have run a 500 ps run with -debug on, but I am unsure of where should 
I look for what it says of relevance -I see the ctab,rtab,dtab xvg's but 
I doubt they are of interest.


m.
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Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

On 18/10/10 03:30, Mark Abraham wrote:

To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:

[ dihedral_restraints ]
; ai   ajak
al  type  label  phi  dphi  kfac  power
; phi C'(n-1) - N - CA - C'
   3
5   7   8   11  -90 752  1


Try mdrun -debug on a short run. What does it have to say about the parameter 
values for this dihedral restraint? Likewise gmxdump -s on the .tpr (though you 
will have to search around for F_DIHRES among other things, probably).


In gmxdump -s output I find:
functype[32]=DIHRES, label=1, power=   1 phi=-9.e+01, dphi= 
7.5000e+01, kfac= 2.e+00)


which seems consistent with what I put in the topology. I looked a bit 
in the dump but it's quite difficult for me to understand what it is 
dumping and how it can be relevant.


If you need other info, the full dump, etc., let me know.

thanks!!
m.
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Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

[ms]

On 18/10/10 12:49, vinothkumar mohanakrishnan wrote:

Dear Mark

I generated the topology using pdb2gmx using dce.pdb. i checked the .top
file and i contains necessary .itp files. the error message that i get is
given below. any help is highly appreciated.


What Mark meant is that you should copy-and-paste here the actual 
commands you typed, and the relevant file lines.


m.
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Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

On 18/10/10 13:06, Mark Abraham wrote:

On 18/10/2010 10:53 PM, ms wrote:

On 18/10/10 03:30, Mark Abraham wrote:

To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:

[ dihedral_restraints ]
; ai aj ak
al type label phi dphi kfac power
; phi C'(n-1) - N - CA - C'
3
5 7 8 1 1 -90 75 2 1


Try mdrun -debug on a short run. What does it have to say about the
parameter values for this dihedral restraint? Likewise gmxdump -s on
the .tpr (though you will have to search around for F_DIHRES among
other things, probably).



I have run a 500 ps run with -debug on, but I am unsure of where
should I look for what it says of relevance -I see the ctab,rtab,dtab
xvg's but I doubt they are of interest.


There should be a much larger .log file, probably named differently.
Check what it reports about dihedral restraints - text searching will be
your friend, here.


Found - mdrun0.log . It's a 4.2 Gb file (argh), I am now trying to grep 
it and see.


m.

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Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

On 18/10/10 13:06, Mark Abraham wrote:

On 18/10/2010 10:53 PM, ms wrote:

On 18/10/10 03:30, Mark Abraham wrote:

To enforce chirality in such a toy, I thought that a simple
(naive?) but functional idea could be that of enforcing a not-
too-hard and wide-bottomed dihedral restrain on the phi angle,
like that:

[ dihedral_restraints ]
; ai aj ak
al type label phi dphi kfac power
; phi C'(n-1) - N - CA - C'
3
5 7 8 1 1 -90 75 2 1


Try mdrun -debug on a short run. What does it have to say about the
parameter values for this dihedral restraint? Likewise gmxdump -s on
the .tpr (though you will have to search around for F_DIHRES among
other things, probably).



I have run a 500 ps run with -debug on, but I am unsure of where
should I look for what it says of relevance -I see the ctab,rtab,dtab
xvg's but I doubt they are of interest.


There should be a much larger .log file, probably named differently.
Check what it reports about dihedral restraints - text searching will be
your friend, here.

Mark


Thanks a lot. As far as I can see I see an endless amount of the following:

dihres[0]: 2 4 6 7 : phi=-2.239583, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[1]: 7 9 11 12 : phi=-2.264564, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[2]: 12 14 16 17 : phi=-2.286253, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[3]: 17 19 21 22 : phi=-2.285502, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[4]: 22 24 26 27 : phi=-2.325288, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[5]: 27 29 31 32 : phi=-2.333271, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[6]: 32 34 36 37 : phi=-2.344587, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[7]: 37 39 41 42 : phi=-2.359801, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[8]: 42 44 46 47 : phi=-2.347612, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[9]: 47 49 51 52 : phi=-2.375774, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[10]: 52 54 56 57 : phi=-2.370417, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[11]: 57 59 61 62 : phi=-2.385128, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[12]: 62 64 66 67 : phi=-2.411767, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[13]: 67 69 71 72 : phi=-2.383690, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[14]: 72 74 76 77 : phi=-2.444273, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[15]: 77 79 81 82 : phi=-2.391789, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[16]: 82 84 86 87 : phi=-2.416251, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[17]: 87 89 91 92 : phi=-2.419053, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[18]: 92 94 96 97 : phi=-2.441001, dphi=1.308997, kfac=20.00, 
power=1, label=1
dihres[19]: 97 99 101 102 : phi=-2.437035, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[20]: 102 104 106 107 : phi=-2.405856, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[21]: 107 109 111 112 : phi=-2.430783, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[22]: 112 114 116 117 : phi=-2.405508, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[23]: 117 119 121 122 : phi=-2.386797, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[24]: 122 124 126 127 : phi=-2.388632, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[25]: 127 129 131 132 : phi=-2.419342, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[26]: 132 134 136 137 : phi=-2.396203, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[27]: 137 139 141 142 : phi=-2.409687, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[28]: 142 144 146 147 : phi=-2.372591, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[29]: 147 149 151 152 : phi=-2.376767, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[30]: 152 154 156 157 : phi=-2.355252, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[31]: 157 159 161 162 : phi=-2.356343, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[32]: 162 164 166 167 : phi=-2.344373, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[33]: 167 169 171 172 : phi=-2.337336, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[34]: 172 174 176 177 : phi=-2.299121, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[35]: 177 179 181 182 : phi=-2.294940, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[36]: 182 184 186 187 : phi=-2.297313, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[37]: 187 189 191 192 : phi=-2.287532, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[38]: 192 194 196 197 : phi=-2.255120, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[39]: 197 199 201 202 : phi=-2.221712, dphi=1.308997, 
kfac=20.00, power=1, label=1
dihres[40]: 202 204 206 207 : phi=-2.115131, dphi=1.308997, 
kfac=20.00, power=1, label=1


Now, the 1.308997 value stays fixed and seems to be the radiants value 
of the 75 degrees dphi parameter I've put in the topo

Re: [gmx-users] Simulation parameter problem about protein unfolding

[ms]

On 18/10/10 13:12, Chen wrote:



At 2010-10-18 16:38:30??"David van der Spoel"  wrote:



On 2010-10-18 06.56, chris.ne...@utoronto.ca wrote:
Generally, forcefields are not parameterized for temperatures other than
298K, so simulations are not expected to reproduce the expected
properties (like boiling water and the correct temperature denaturation
of proteins).

There's almost certainly other issues here (including the fact that I'm
entirely sure that you can get a lot more than 24 ns of simulation on a
54 aa protein; and 26 atom of pressure seems pretty arbitrary) but it
will come down to this eventually.

Just because you found a paper in which they get a denatured state does
not imply that they got the correct denatured state.


There is no correct denatured state. There are infinitely many. Check
out recent work on NMR of "unfolded" proteins.



I thought about the unfolding state space is huge. I just wonder
whether the relative low radius of gyration value space sampled by us is caused
by some error setting in MD parameters. If no one here finds there's problem in
my MD parameters, then I can keep going. Thanks!


In theory, you should be able to calculate the expected gyration radius 
of a purely non-interacting random chain (which one can take as the 
limit of an unfolded protein). given the distance between monomeric 
units (i.e. C-alpha for example here). It is a three-dimensional random 
walk.

http://en.wikipedia.org/wiki/Radius_of_gyration#Molecular_applications

Doing the calculation for the equation of the three-dimensional random 
walk of your 54 aa protein, with N=54 and a=0.35 nm, it turns out that 
the expected gyration radius is:


>>> (np.sqrt(54) * 0.35) * (1/np.sqrt(6))
1.0503 nm

So, yes, your average protein gyration radius is consistent with the 
protein being a random coil -that is, unfolded.


In truth your random coil ball should be a bit larger because in the 
calculation we ignore the chain self-avoidance, but on the other hand we 
have that a protein chain is not completely non-self-interacting, for 
obvious reasons. Therefore it seems you can conclude that your protein 
is reasonably close to being unfolded.


Hope it helps,
Massimo

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Re: [gmx-users] Intrinsically disordered proteins

[ms]

On 18/10/10 14:26, #ZHAO LINA# wrote:

Hi,

1. For those intrinsically disordered proteins, the sequence is known, how the 
simulations will be set up, I mean, the first PDB will be needed, how to get 
this one? (Ideally, not necessarily to be practical)

2. suppose I got a PDB, there were several models there, let's say 16, is it 
acceptable to just take one, say model 1?

Thanks for any answering,


That's a theoretical question which has no real "true" answer, given 
that there is no "true" structure for an IDP, but only an ensemble of 
structures.


I've seen different approaches, from using ROSETTA predictions to simply 
using random coil structures, to carefully picking ensembles from 
previous experimentally-restrained simulations. Pick up your favourite 
approach in the literature, also taking into account what you want to do.


m.

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Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

On 18/10/10 13:06, Mark Abraham wrote:

On 18/10/2010 10:53 PM, ms wrote:

On 18/10/10 03:30, Mark Abraham wrote:


Mark,

Thanks a lot for cc'ing me the bugzilla report. Do you think it is 
related to the problems I have? (well, for sure bugs can't help, but...)


thank you!

m.


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Re: [gmx-users] Tables with forcefield

[ms]

On 27/09/10 21:18, Sai Pooja wrote:

Thanks M!

I am using the standard 6-12 tables available with the gromacs package. For
-table and -tablep options to start with.

I want to understand 1 thing. The forcefield files and the topology file
specifies sigma and epsilon parameters. If I change the combination rule to
1 in the forcefield.itp file, and use tables, how does gromacs convert the
sigma, epsilon values in the topology file to C6 and C12?


This is explained in the manual. specificially section 6.7.2



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Re: [gmx-users] problem in executing genbox command

[ms]

On 06/11/10 07:46, Mark Abraham wrote:

On 6/11/2010 4:02 PM, bharat gupta wrote:

Hi all ,

Whenever i am running the genbox command I am getting the following
error :-


genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

:-) G R O M A C S (-:

Segmentation fault (core dumped)


The most likely scenario is some shared library is not available when it
should be. That means the environment in which you ran the above command
is different from the one in which GROMACS was built. That means
most/all GROMACS commands will fail. A possibility is that there's a bug
in GROMACS, but I doubt it. Do other GROMACS commands, or other genbox
runs work?


A missing library should show explicitly as such, not as a segfault. I 
suspect some compilation glitch. What compiler did you use? On what system?


A good idea would be to run the command through gdb.


Mark



Can anybody tell me whats the reason for such an error ...

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[gmx-users] trjconv, pbc and breaking of multiple peptides

[ms]

Hi,

I am doing REMD simulations of multiple homopolymeric peptides in a PBC 
box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to 
analyze features of the system that require to use g_gyrate to find out 
the moments of inertia of the system, for example.


I understand g_gyrate is one of the few tools that is *not* PBC aware. I 
am trying therefore to correct my REMD trajectories using several 
variants of trjconv, with simple command lines like:


trjconv -f xac_12855257520.xtc -o xac_12855257520_pbcatom.xtc -pbc nojump

...but alas, when I see them with ngmx, the peptides tend to break. I 
tried both pbc nojump and pbc atom, with same results (pbc nojump 
perhaps is a bit worse). I can't use pbc cluster because they're not 
always clustered and I am interested in both the clustered and 
non-clustered states.


I'd like to give more information about that but I don't really know 
what is relevant to debug this kind of issue. I looked in the mailing 
list but (despite multiple woes about pbc nojump etc.) I didn't find a 
helpful thread. Any hint?


thanks!
Massimo

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Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

[ms]

On 09/11/10 21:36, Justin A. Lemkul wrote:

I am doing REMD simulations of multiple homopolymeric peptides in a
PBC box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want
to analyze features of the system that require to use g_gyrate to find
out the moments of inertia of the system, for example.

I understand g_gyrate is one of the few tools that is *not* PBC aware.
I am trying therefore to correct my REMD trajectories using several
variants of trjconv, with simple command lines like:

trjconv -f xac_12855257520.xtc -o xac_12855257520_pbcatom.xtc -pbc nojump

...but alas, when I see them with ngmx, the peptides tend to break. I
tried both pbc nojump and pbc atom, with same results (pbc nojump
perhaps is a bit worse). I can't use pbc cluster because they're not
always clustered and I am interested in both the clustered and
non-clustered states.

I'd like to give more information about that but I don't really know
what is relevant to debug this kind of issue. I looked in the mailing
list but (despite multiple woes about pbc nojump etc.) I didn't find a
helpful thread. Any hint?



There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is often a much better approach, in my experience.


Excellent advice; it seems to do exactly what I want. Thanks a lot!!

Massimo



-Justin


thanks!
Massimo






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Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

[ms]

On 09/11/10 21:36, Justin A. Lemkul wrote:


There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is often a much better approach, in my experience.


I spoke too soon. -pbc mol -center doesn't indeed break molecules, but 
it doesn't seem to always work correctly -I evidently continue to have 
frames where the system is obviously not centered correctly in the box, 
so even if I have a compact conglomerate of my molecules, the calculated 
gyration radius is artificially large (In fact, I discovered the issue 
by looking at the frames with large gyration radiuses).


I am sure it doesn't work correctly because if I visualize the system in 
VMD, enabling periodic copies I see the correct (compact) structure at 
the corners between boxes. - I can provide pictures if needed.


Any idea on how to proceed? I am quite lost. I wouldn't like to rewrite 
g_gyrate by myself :)


thanks!
m.

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Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

[ms]

On 10/11/10 21:34, Justin A. Lemkul wrote:



ms wrote:

On 09/11/10 21:36, Justin A. Lemkul wrote:


There are numerous -pbc options with trjconv; have you tried others? I
have never had luck with -pbc nojump actually working, and -pbc atom
provides no guarantee that molecules will be properly reconstructed.
Using -pbc mol -center is often a much better approach, in my
experience.


I spoke too soon. -pbc mol -center doesn't indeed break molecules, but
it doesn't seem to always work correctly -I evidently continue to have
frames where the system is obviously not centered correctly in the
box, so even if I have a compact conglomerate of my molecules, the
calculated gyration radius is artificially large (In fact, I
discovered the issue by looking at the frames with large gyration
radiuses).

I am sure it doesn't work correctly because if I visualize the system
in VMD, enabling periodic copies I see the correct (compact) structure
at the corners between boxes. - I can provide pictures if needed.

Any idea on how to proceed? I am quite lost. I wouldn't like to
rewrite g_gyrate by myself :)



I presume you're centering on "Protein" in this case?


Yes, sorry for not making it clear.


You can create a
custom index group (perhaps towards the center of one of your peptides)
and center about it. The -center function will locate the center of mass
of the chosen group at the center of the box, so, in a simple case (i.e.
a dimer) you would have two peptides at the corners, but the center of
mass still located at the box center. Choosing one residue of one of the
monomers has, in my experience, solved this issue when centering about
Protein has not worked.


I don't get it.

First, let me see if I understand it correctly. From your explanation 
(and intuition), it seems that the issue is that "center of mass" in a 
periodic environment is ambiguous -there are always (at least) two 
alternate configurations that have the center of mass at the center of 
the box any time, and -center doesn't necessarily choose the most 
compact one (i.e. the one where the box center is closest on average to 
atoms). So, for example, in a 1-D periodic environment, this:


... O|O  O|O ...

is equivalent to this

|   OO   |   OO  ...

the center of mass between the O's being always at the center of the box 
in both cases.


But I don't see how choosing one residue could help -I mean, the 
residues wander practically everywhere in the box during the simulation 
and none of them is privileged ; I don't see why centering only around 
one would be better. It could help if they were only two, but we talk of 
eight objects here (and possibly many more in the future)...


...now I see it: You mean that, since I force to center around one of 
the objects, and if on average it should belong to the cluster, the 
whole thing should be more often than not within the box?


I'm going to try; meanwhile let me know if I got it right (and just in 
case, I wonder how much work is to patch trjconv to "choose" the "right" 
center of mass -I guess it's similar to what -pbc cluster does? I never 
fully understood that option)


m.

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Re: [gmx-users] trjconv, pbc and breaking of multiple peptides

[ms]

On 10/11/10 22:28, Justin A. Lemkul wrote:

First, let me see if I understand it correctly. From your explanation
(and intuition), it seems that the issue is that "center of mass" in a
periodic environment is ambiguous -there are always (at least) two
alternate configurations that have the center of mass at the center of
the box any time, and -center doesn't necessarily choose the most
compact one (i.e. the one where the box center is closest on average
to atoms). So, for example, in a 1-D periodic environment, this:

... O|O O|O ...

is equivalent to this

| OO | OO ...

the center of mass between the O's being always at the center of the
box in both cases.



Correct.


But I don't see how choosing one residue could help -I mean, the
residues wander practically everywhere in the box during the
simulation and none of them is privileged ; I don't see why centering
only around one would be better. It could help if they were only two,
but we talk of eight objects here (and possibly many more in the
future)...

...now I see it: You mean that, since I force to center around one of
the objects, and if on average it should belong to the cluster, the
whole thing should be more often than not within the box?



That's it. Take, for example, peptides A, B, and C. Peptide A is a
nucleation point for B and C to attach. Conceivably, trjconv could
choose a "center" that involves C on one "side" of the box and A+B on
the other. The whole protein is still "centered" by its criteria.

If, physically, A is in the core of the aggregate, then I could choose
some residue in peptide A and choose to center about it. There is no
other alignment that trjconv can assign, other than to place that chosen
residue of peptide A right in the middle of your unit cell. It can't be
broken any other way.


It seems to work right this time! Beautiful trick. Thank you again so 
much -if I could, I would give you a big hug. I am still a newbie with 
molecular simulations (my Ph.D. was on experimental biophysics) and I 
still fall into a lot of easy traps!


cheers,
M.

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Re: [gmx-users] protein folding

[ms]

On 22/11/10 11:09, mohsen ramezanpour wrote:

Dear All

I am searching for a tutorial for  learning how to do protein folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.


I don't think so because managing to fold a protein in a MD simulation 
is no easy task. In theory, if you have a lot of patience and a lot of 
computational resources, it's no different from a normal MD simulation, 
but good luck even getting *close* to a folded state.


So, it all depends on what you want really to know, and in this case 
several techniques may help you (REMD, metadynamics, etc.) but I think 
you have to read a lot of literature to make up your mind on such stuff.


M.


Thanks in advance
Sincerely
Mohsen





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Re: [gmx-users] .itp for simple atom

[ms]

On 23/11/10 09:43, leila separdar wrote:

I am beginner with gromacs I want to simulate a system of 100 Argon atom
with Lennard Jones force field but I do not know how to make .itp file I
have made this lines but it made error. could anybody hep me?


Telling what errors come out would help.



[ atomtypes ]
;name  at.num   mass  charge   ptypesigmaepsilon
AR   1839.948 0.0A 2.54129e-011.58992e-01

[ nonbond_params ]
   ; ij func  c6   c12
; Encad uses strict combination rules, so no need for explicit parameters

[ pairtypes ]
   ; ij func cs6  cs12
; 1,4 interactions are calculated automatically, using fudge factors.
; (In the current version, the factors are 0.0, meaning no 1,4
interactions).





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[gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

[ms]

Dear GROMACS users,

I am trying to visualize a trajectory with hundreds of peptides which 
come and go out and in the faces of the periodic box. Problem is, when 
they cross the periodic boundary, the visualization software (I tried 
both VMD and PyMol) create visual artefacts by visualizing nonsensically 
long bonds crossing the box -which I understand, since the algorithms 
seem to have no clear notion of PBC.


Using -pbc nojump or similar, given my experience with identical systems 
only containing less peptides, is not going to work (peptides are going 
to be "broken").


Since all I want is some nice snasphot of the trajectory to show and not 
analysis, I feel that a much easier solution would be to find a setting 
in the visualization softwares that simply do not visualize bonds longer 
than a threshold. However I can't find such a setting. Does one exist? 
Does a "PBC mode" exist? What kind of solution do you propose? I googled 
quite a bit but I couldn't find much.


Thanks,
Massimo

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Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[ms]

Ok, I can update this situation (see below quote):

On 18/10/10 03:30, Mark Abraham wrote:

And then, I read on the Gromacs website *this*
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
" 2. The manual is a bit unclear about whether this type of
dihedral restraint is stable for use near 180 degrees. Chris
Neale has found that everything appears to behave normally and
as expected over the entire range of dihedral angles including
180 degrees. However, one must avoid the situation in which the
actual dihedral is close to 180deg away from the restrained dihedral."

And I know that somehow the potential is discontinuous and/or
anyway not intended to be well-behaved everywhere:
http://www.mail-archive.com/gmx-users@gromacs.org/msg12353.html

">  On Tue, Feb 26, 2008 at 11:37 AM, David Mobley<[EMAIL
PROTECTED]>  wrote:

  The other way of putting what Mark said is that phi is

only meaningful on some range (-pi to pi, or 0 to 2pi, depending
on how you define it)

  and so what you require is that the potential be

harmonic for the

  region in which phi is meaningful. You don't care what

happens outside that. Or, in this case, you handle the issue by
mapping phi values  outside the allowed range back into
that allowed range."

(I don't get what does it mean to "map back" phi values, by the way).

I am no MD expert, so maybe my hypothesis is totally off, but I
am reasonably sure that either I do not understand correctly how
dihedral restraints work, or I am suffering by the discontinuity
of the way the potential is implemented (Or both). I would like
to know:


I managed to patch the dihedral restraining part so to mitigate the 
issue. The problem lied in the 180-degrees discontinuity in the force, 
where it jumps from a highly positive to a highly negative value, like 
(Y=force, X=angle):


   /|
  / |
 /  |  /
/   | /
|/

I have cut the ends close to the phi=180 and "connected" the force 
values like that:


  /\
 /  \/
/\  /
  \/

and then redefined the energy to be the integral of that line.

This way it works -you can have decent restraining along all phi angles 
without risking to freeze, provided the energy barrier at 180 is not too 
high.


The patch looks really ugly -it has been kludged in quite a hurry and... 
well, looks obscene, but if someone wants to look at it, let me know!


m.

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Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

[ms]

On 23/11/10 17:00, Mark Abraham wrote:

If you only want a snapshot, then simply write a single chosen frame to
a .gro or .pdb using trjconv. Load only that into VMD, and it won't
generate PBC-crossing bonds.

If you want a movie, then there I seem to recall that there is a VMD
option to generate bonds for each frame, and not to use those from the
first frame. Ask their mailing list. Such bonds will not traverse the
PBC, obviously.


Cool, thanks! I'll dig it.
I'd really hope there is a pymol option as well, I'll see :)


There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break.


Yep, but if they appear broken because they are at the pbc boundaries is 
no big deal. The problem (and with this I answer also Florian Dommert) 
is that using -pbc tends to "break" stuff *inside* the box.


thanks,
M.



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Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

[ms]

On 23/11/10 17:00, Mark Abraham wrote:

If you want a movie, then there I seem to recall that there is a VMD
option to generate bonds for each frame, and not to use those from the
first frame. Ask their mailing list. Such bonds will not traverse the
PBC, obviously.


Just for the record: It seems that typing "mol bondsrecalc all" at the 
VMD Tk console and refreshing the visualization works to "sanitize" a frame.


thanks!
m.


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Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

[ms]

On 23/11/10 17:00, Mark Abraham wrote:

If you only want a snapshot, then simply write a single chosen frame to
a .gro or .pdb using trjconv. Load only that into VMD, and it won't
generate PBC-crossing bonds.

If you want a movie, then there I seem to recall that there is a VMD
option to generate bonds for each frame, and not to use those from the
first frame. Ask their mailing list. Such bonds will not traverse the
PBC, obviously. There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break.


For PyMol, here is the solution:
http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg07721.html

thanks for pointing!
m.

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Re: [gmx-users] mdrun crashed with tables

[ms]

On 23/11/10 21:42, Sai Pooja wrote:

Hi,

I run a simulation of a protein in water(tip3p) system using charmm
forcefield. I have specified the following energy groups:
Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype
to User and VdW to Cut-off. I then generate tables as specified in the
manual. To test the validity of these tables, I standard Coulomb and LJ6,12
tables.
I generate 4 tables - table.xvg, table_Protein_SOL.xvg, table_SOL_SOL.xvg
and tablep.xvg (all identical)
When I run grompp I get no errors. When I run mdrun, it stops after the
first step as LINCS fails to converge.
I run the same simulation by changing the Coulombtype to Cut-off and without
the tables and it runs.

Can you suggest what could be going wrong?


Are the tables correct? The derivative is correct? Signs, units, etc.? 
How did you generate them?


Often the devil is in the most trivial -and therefore overlooked- errors.

What does the mdrun log say?

In any case, you can try using the -debug option of mdrun and have a 
look at the *interpolated* tables in output to see if they are 
consistent with your intentions (warning: using -debug can spit out 
gigabytes of stuff).



(python script)
Command used: cmd += '(%s/mdrun_mpi -s rex_%d.tpr -e rex_%d -c after_rex_%d
-cpi restart%d -cpo restart%d -cpt 0.1 -append -g rexlog%d -x rextraj%d
-table table.xvg table_Protein_SOL.xvg table_SOL_SOL.xvg -tablep tablep.xvg

/dev/null); ' %(GROMPATH,i,i,i,i,i,i,i)


I tried this in two ways -
1) specified [ nonbonded_param ] for all Protein atoms and tip3p atoms
2) Not specifying them separately

Thanks and regards
Pooja




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Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

[ms]

On 24/11/10 02:47, Mark Abraham wrote:

On 24/11/2010 5:04 AM, ms wrote:

On 23/11/10 17:00, Mark Abraham wrote:

There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break.


Yep, but if they appear broken because they are at the pbc boundaries
is no big deal. The problem (and with this I answer also Florian
Dommert) is that using -pbc tends to "break" stuff *inside* the box.


That can't be true in general. Use of one of the five different -pbc
options, possibly with -center and -ur, possibly over several
invocations has always worked for anything I've wanted. However it's
hard to answer an assertion that something is broken if you don't know
what the person has tried :-)


You are absolutely right, but well, it was not needed for the aestethic 
purposes so far required :)


Of course if and when needed for analysis, I'll try harder with trjconv 
-pbc arcanes.


thanks!
m.

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Re: [gmx-users] Replica exchange

[ms]

On 27/11/10 17:49, Sai Pooja wrote:

Hi,

I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I supply a table name different from
table_Protein_SOL.xvg for protein solvent interactions, like
rex0_table_Protein_SOL.xvg, I get an error -
Fatal error:
Library file in current dir nor  not found table_Protein_SOL.xvgin default
directories.
(You can set the directories to search with the GMXLIB path variable)
For more information and tips for troubleshooting, please check the GROMACS
To oversome this limitation, I am using something like this:

[pseudocode]
for r 1 to n:
copy rex_r_Protein_SOL.xvg table_Protein_SOL.xvg
mdrun -s .. -table table.xvg -table table_Protein_SOL.xvg ...

Will mdrun be able to run with separate table parameters in this way?


I can use different tables with names in a fashion like:
table_B_30_70_0.4_GroupA_GroupB.xvg

(where GroupA and GroupB can be whatever you want)

Then the mdrun line is
mdrun ...  -table table_B_30_70_0.4.xvg

and then mdrun takes care of looking after the GroupA_GroupB , 
GroupB_GroupC etc. tables, depending on your .mdp file.


Hope it helps,
M.

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Re: [gmx-users] Replica exchange

[ms]

On 27/11/10 17:49, Sai Pooja wrote:

Hi,

I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I supply a table name different from
table_Protein_SOL.xvg for protein solvent interactions, like
rex0_table_Protein_SOL.xvg, I get an error -
Fatal error:
Library file in current dir nor  not found table_Protein_SOL.xvgin default
directories.
(You can set the directories to search with the GMXLIB path variable)
For more information and tips for troubleshooting, please check the GROMACS
To oversome this limitation, I am using something like this:

[pseudocode]
for r 1 to n:
copy rex_r_Protein_SOL.xvg table_Protein_SOL.xvg
mdrun -s .. -table table.xvg -table table_Protein_SOL.xvg ...


Since my previous mail was perhaps confusing, I clarify: You should be 
able to use whatever follows the convention:


table_whateveryoulike_groupA_groupB.xvg
table_whateveryoulike_groupA_groupC.xvg
table_whateveryoulike_groupB_groupC.xvg
...

and you just use

mdrun ... -table table_whateveryoulike.xvg

*without* groupA_groupB ; because then it's mdrun's job (well, grompp 
actually, probably -it's all scripted so I don't remember now!) to look 
after the actual tables' names from the couples defined in the .mdp


Hope it helps,
M.
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[gmx-users] [OT] Generate random coil protein conformations?

[ms]

Hi,

Sorry for the offtopic but my google-fu is apparently abandoning me. I 
am looking for a fast way to generate random coil protein configurations 
to use as startpoints for several simulations I'd like to do.


All I managed to find is:
- FOLDTRAJ which seems unavailable and discontinued
- the server at unfolded.uchicago.edu, which actual working part ( 
http://z-appserver.cti.depaul.edu/~unfolded/start.html ) seems 
unavailable as well.


Anyone has working suggestions for that? I am quite sure there must be 
such a package, yet I can't find it... dumb me probably.


cheers,
M.

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Re: [gmx-users] [OT] Generate random coil protein conformations?

[ms]

On 05/12/10 00:26, Mark Abraham wrote:

Sorry for the offtopic but my google-fu is apparently abandoning me. I am 
looking for a fast way to generate random coil protein configurations to use as 
startpoints for several simulations I'd like to do.

All I managed to find is:
- FOLDTRAJ which seems unavailable and discontinued
- the server at unfolded.uchicago.edu, which actual working part ( 
http://z-appserver.cti.depaul.edu/~unfolded/start.html ) seems unavailable as 
well.

Anyone has working suggestions for that? I am quite sure there must be such a 
package, yet I can't find it... dumb me probably.



I dunno if it will help, but Googling with "self-avoiding Gaussian walk" might 
help - since that's what a random coil is.


Thanks, nice tip -even if I doubt that a real RC is truly Gaussian in 
angle distribution, it is good enough for what I want to do -I can 
script Pymol about that.


m.

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Re: [gmx-users] Change in structure after solvation_Gromacs

[ms]

On 05/12/10 10:39, swagata chakraborty wrote:

I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a sheet.
Please suggest where I am going wrong since the structure shouldnot change
after solvation.


You're not giving nearly enough detail (what is the dmso/water ratio? 
what is your .mdp file?) etc.


In any case, it wouldn't be the first time that simulations and 
experiments disagree. How do you *know* that structure shouldn't change? 
Have you tried using another force field, like OPLS?


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Re: [gmx-users] Change in structure after solvation_Gromacs

[ms]

On 05/12/10 13:20, Justin A. Lemkul wrote:



ms wrote:

On 05/12/10 10:39, swagata chakraborty wrote:

I was trying to run MD simulation of my protein in DMSO. I used the
force
field ffG53a6 and did the energy minimization after solvating the
protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a
sheet.
Please suggest where I am going wrong since the structure shouldnot
change
after solvation.


You're not giving nearly enough detail (what is the dmso/water ratio?
what is your .mdp file?) etc.

In any case, it wouldn't be the first time that simulations and
experiments disagree. How do you *know* that structure shouldn't
change? Have you tried using another force field, like OPLS?



This might just be a visualization artifact, something that gets posted
here routinely. Some slight structural changes may have occurred during
EM, such that the visualization program guess sheet instead of loop.
53A6 does tend to favor extended structures, but I would only suggest
something is wrong if (1) a real simulation is conducted and the
spurious secondary structure persists and (2) real analysis is done
(like DSSP or STRIDE) to conclude the secondary structure, rather than
just looking at it, as all visualization software uses different
heuristics to assign structures. It does not make for convincing evidence.



You are absolutely right (as almost always you are!), yet more detail, 
the better. I'd say that visualizing it in Pymol using the dss command 
to give the DSSP assignment could help.


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Re: [gmx-users] Re: polymer simulations in gromacs

[ms]

On 05/12/10 19:41, Justin A. Lemkul wrote:


Please keep all Gromacs-related correspondence on the gmx-users list. I
am not a private help service.

I do not do polymer simulations, nor do I have any real clue as to how
to help you, aside from suggesting the following, which may or may not
be relevant:

http://www.gromacs.org/Documentation/How-tos/Polymers
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

I am CC'ing this message to the list. Please keep all further posts
there, as perhaps someone can actually help you.

-Justin

Björn Nadrowski wrote:

Hi Justin, I just found out that you are simulating polymers using
gromacs. I would like to do the same stuff, but from a much less
molecular angle.
I am the only one here that does that stuff, so I have to jump through
all the loops myself, and the gromacs loop is really tiny and hard to
jump through.
Ideally, I would just like to define my polymer as a succession of
identical nodes, that have a user(i.e. defined by me) interaction
potential (essentially hard core repulsion with an intermedeiate
attractive regime), some 3-node angle stiffness term, friction (no
water! Just the polymers with friction!), position restraints (all
bonds between the nodes should be constrained to have the same
length), and
some boundary conditions.
How would I go about that?
I have scanned the documentation, but I am beaten to death by its
volume, where most of it concerns stuff I am not
interested in. Ideally, I would like to represent my nodes as some
kind of idealistic atom with said interactions. However, I do not find
the part where I define such an atom, or how to do that. Can you point
me to some source where I might get a nice simple tutorial of how to
define such an elementary node, and its interactions?



Hi Bjoern,
Your experience is much like mine -I am actually doing something very 
similar, a coarse grain to model proteins which has very very similar 
features (I even suspect we're starting from the same literature, given 
the description). My advice is:


- Read the documentation. Multiple times. Understand it. *All* of it 
concerns stuff you *will* be interested in (apart perhaps some specific 
analysis tool, but even there...). Yes, it's long, but there's no hope 
of going anywhere without knowing it.
- Look at how residues and force fields are defined. Learn to create 
your own force field. The easiest thing is probably taking an existent 
force field, duplicate it and then work on the copy customizing it to 
your liking (That's what I did).
- Also, look at how protein residues are defined for use with pdb2gmx 
etc. - even if you are designing a non-protein polymer, it all basically 
starts from there, you then edit the residues etc. until you get the 
"unit" you want.
- Learn about tables and tabulated potentials if VdW functions are not 
enough.

- Learn about charge groups, energy groups etc.
- Remember that hardcore repulsion doesn't play well with MD 
integration: you'll spend a lot of time tuning it to be stiff enough but 
not too much to make your system explode

- About friction, do you mean Langevin dynamics?
- Do a lot of tests :)

It's very general advice, I know, but there's no real tutorial for such 
a thing, every custom model is... custom, and everyone, wanting 
different things, is quite on its own.


Best of luck! It took me about 1 - 1.2 years to get the model begin to 
work, so be patient and don't despair!


cheers,
M.

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Re: [gmx-users] LJ Plot

[ms]

On 06/12/10 23:26, nishap.pa...@utoronto.ca wrote:

Quoting "Justin A. Lemkul" :

I actually want to plot my simulation with ad without the attractive
term C6 of van der Waals and superimpose them to see the difference.


The expression "plot my simulation" makes no sense. You don't plot a 
simulation, you plot variables calculated from a trajectory.


Also, what does it mean "with and without the attractive term"? You 
perhaps want to *do* two different simulations?




nishap.pa...@utoronto.ca wrote:

Quoting "Justin A. Lemkul" :

How does sigeps read the input file? I tried using sigeps to plot LJ
for different solutes in solvent and it gives me the same C6 and C12
value, when it runs, which seems a weird.

c6 = 1.0e-03, c12 = 1.0e-06
sigma = 0.0, epsilon = 0.0
Van der Waals minimum at 0, V = nan


g_sigeps does not take any input file. It produces an LJ curve based
on command line parameters. I guess this is not what you are after,
although that's exactly what it sounded like from your last post.
Perhaps you need to re-phrase your question. If you just want to plot
van der Waals energy terms, use g_energy to pull them out of the .edr
file.

-Justin



Is it the default?



nishap.pa...@utoronto.ca wrote:

Hello,

Is there an option to plot Lennard Jones potential? I tried looking
through the list and manual but I did not find any suggestions on
how I could plot a LJ 6-12 potential plot.



g_sigeps

-Justin


Nisha




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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] LJ Plot

[ms]

On 07/12/10 03:06, nishap.pa...@utoronto.ca wrote:

Quoting ms :

I did two different simulation. One with van der Waals attractive term
and one without van der Waals attractive term. And so to see the
difference between the LJ potential between the two simulation I wanted
to plot the LJ potential for both the simulations and superimpose them.
Because if there is no attraction LJ-12 (i.e. 1/r^-6 set to zero )LJ
potential plot would be different than the one with LJ 6-12 potential.


Perhaps you just want to use g_energy and plot the LJ terms of your 
simulations during time ?



On 06/12/10 23:26, nishap.pa...@utoronto.ca wrote:

Quoting "Justin A. Lemkul" :

I actually want to plot my simulation with ad without the attractive
term C6 of van der Waals and superimpose them to see the difference.


The expression "plot my simulation" makes no sense. You don't plot a
simulation, you plot variables calculated from a trajectory.

Also, what does it mean "with and without the attractive term"? You
perhaps want to *do* two different simulations?



nishap.pa...@utoronto.ca wrote:

Quoting "Justin A. Lemkul" :

How does sigeps read the input file? I tried using sigeps to plot LJ
for different solutes in solvent and it gives me the same C6 and C12
value, when it runs, which seems a weird.

c6 = 1.0e-03, c12 = 1.0e-06
sigma = 0.0, epsilon = 0.0
Van der Waals minimum at 0, V = nan


g_sigeps does not take any input file. It produces an LJ curve based
on command line parameters. I guess this is not what you are after,
although that's exactly what it sounded like from your last post.
Perhaps you need to re-phrase your question. If you just want to plot
van der Waals energy terms, use g_energy to pull them out of the .edr
file.

-Justin



Is it the default?



nishap.pa...@utoronto.ca wrote:

Hello,

Is there an option to plot Lennard Jones potential? I tried looking
through the list and manual but I did not find any suggestions on
how I could plot a LJ 6-12 potential plot.



g_sigeps

-Justin


Nisha




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Nose-hoover T-coupling in REMD

[ms]

On 24/12/10 10:36, David van der Spoel wrote:

On 2010-12-24 11.04, Mark Abraham wrote:

On 22/12/2010 5:44 PM, Qin Qiao wrote:

Dear all,

I posted yesterday but didn't get answer..I guess it's due to my wrong
approach to ask. I would like to explain more and hope I would get
your help.

I'm doing an REMD, and want to have a strong temperature coupling to
make sure every replica is at its target temperature. I guess I could
do it by setting tau_t small in the Nose-hoover T coupling, but there
will come the warning in Gromacs.

I maxwarned the warning to proceed, and find the temperature is ok,
but I am not sure whether it will introduce some artifacts in the
simulation and what kind of artifacts. Could you tell me? Thanks a lot.


The temperature coupling algorithms are discussed in the literature,
when they were derived (citations in GROMACS manual) and subsequently. I
suggest you do your own homework there. The use of REMD is more or less
irrelevant to the trade-offs when deciding what temperature coupling
scheme to use.


That is correct, but do not use Berendsen! There is a recent paper from
the Garcia group (IIRC) about the effect of Berendsen coupling on REMD
sampling. Not good.

Mark


I'm not an expert, but isn't Berendsen usually not used because it 
doesn't give a correct ensemble? I may be partial because I personally 
know Giovanni Bussi, but it seems from what I've heard that v-rescale is 
the best choice usually.


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Re: [gmx-users] Nose-hoover T-coupling in REMD

[ms]

On 24/12/10 12:26, David van der Spoel wrote:


I'm not an expert, but isn't Berendsen usually not used because it
doesn't give a correct ensemble? I may be partial because I personally
know Giovanni Bussi, but it seems from what I've heard that v-rescale is
the best choice usually.


V-rescale is a good choice. Berendsen not only gives you the wrong
ensemble but it also biases the energy distribution to lower energies.


Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to 
less confusion if it is removed? :)


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Re: [gmx-users] Nose-hoover T-coupling in REMD

[ms]

On 25/12/10 02:12, Qin Qiao wrote:

Thanks a lot!

It says Nose-hoover coupling generates the correct canonical ensemble, and
that's the reason why I used it. I wonder whether v-rescale can also get the
correct ensemble. Could you tell me?


As far as I know v-rescale should generate a correct ensemble.

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Re: [gmx-users] Nose-hoover T-coupling in REMD

[ms]

On 25/12/10 02:12, Qin Qiao wrote:


Thanks a lot!

It says Nose-hoover coupling generates the correct canonical ensemble, and
that's the reason why I used it. I wonder whether v-rescale can also get
the
correct ensemble. Could you tell me?



As far as I know v-rescale should generate a correct ensemble.


On 25/12/10 12:40, Qin Qiao wrote:
> I'm not sure, since actually kinetic energy should have fluctuation, 
and the

> v-rescaling may suppress the fluctuation..
>

(PLEASE don't top post!!)

Well, the thermostat author, who I happen to know, says it generates the 
right ensemble. :) I'm not an expert so I can't say if it's true, but if 
you like you can read the original papers, linked here:


http://sites.google.com/site/giovannibussi/Research/algorithms#TOC-A-stochastic-velocity-rescaling-the

cheers,
m.

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Re: [gmx-users] making maxwarn a hidden option

[ms]

On 29/12/10 21:57, chris.ne...@utoronto.ca wrote:

That sounds reasonable. I don't like hidden options except for when they
are associated with manuscripts that have not yet been published.


As a "young" Gromacs user and an "old" free software user and developer, 
I wholeheartedly disagree with hiding or making -maxwarn more difficult 
-or whatever other option, FWIW. It would really annoy me, frankly. If 
there is something I truly dislike, it is software (and developers) that 
behave like nannies to their users.


If an option is available, it should be fully documented like everything 
else. There is nothing more infuriating than discovering that you could 
have done something you wanted to do, if only it was documented. Now, I 
reckon that warnings should be verbose and that it should be explained 
in detail what each warning means, but it's up to the user to decide 
what to do.


In short: If you respect your users, you don't treat them like children 
you hide the candies from.


Sorry for the rant and happy new year :)

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Re: [gmx-users] making maxwarn a hidden option

[ms]

On 29/12/10 23:47, Justin A. Lemkul wrote:


I think the root problem boils down to a lack of documentation of this
feature. For most routine use, -maxwarn should not be used, similar to
-missing with pdb2gmx.


Yes, but it depends. In my systems I routinely have to use both to get 
the system right, because it's a custom coarse grain and both programs 
spit warnings due to quirks of my (surely non-usual) system -that I am 
aware of and (as far as I know and I tested) are safe to ignore.



It is your last safeguard when fatal errors
occur, but if it is implied that using it is somehow routine or
convenient, then we begin to undermine the use of all those informative
notes and warnings that grompp prints.


Well, no: grompp should instead print *more* stuff, and explain more in 
detail what the warning refers to, showing (for example) the line of the 
.mdp or .top file it refers to and stuff like that, and pointing to an 
exhaustive manual section to understand it.


This doesn't undermine: quite the opposite, it empowers the user with 
*knowledge* that then will use to *decide* what to do.



Looking through the grompp help description, there is no mention of this
feature, and the one-line description is somewhat vague. Perhaps the
best solution is simply to add some documentation, in addition to the
wiki entry I created.

The description of this flag is currently "Number of allowed warnings
during input processing." Perhaps it should say something like "Number
of allowed warnings during input processing. Not for normal use and may
generate unstable systems." I would also think that a description should
be added to the grompp -h text, like:

"The -maxwarn option can be used to override warnings printed by grompp
that otherwise halt output. In some cases, warnings are harmless, but
usually are not. The user is advised to carefully interpret the output
messages before attempting to bypass them with this option."

If that sounds agreeable, I'll put in an enhancement request.


This makes a lot of sense and I agree in full.

Thanks,
Massimo

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Re: [gmx-users] making maxwarn a hidden option

[ms]

On 30/12/10 01:07, Justin A. Lemkul wrote:

It sounds very much like your systems are in the minority - those for
which -maxwarn is essential :)


Oh yes. But... you don't want to discriminate minorities!! :D


What I meant was that -maxwarn allows a user to casually bypass that
which grompp is already printing, something that has caused problems at
least 2 or 3 times now in the last week, I believe.

I know of at least one commonly-used tutorial supplies example grompp
commands with -maxwarn and no explanation as to what it's doing or why
it's being invoked. What we need to do is avoid this blind practice. I
think grompp has a sufficient level of verbosity for most cases. In most
(if not all) instances, the lines in the .mdp and/or .top are clearly
indicated.


Well, you will *never* change user's practice unless you change the head 
of your users. You can put all the hoops and loops but never 
underestimate the potential of your users to ignore the obvious and take 
the most direct, even if dangerous, road. All hoops and loops you put 
just annoy the people that know and don't need such difficulties. :)


I think that, simply, users should be warned and informed in full. After 
that, it's their choice and their responsibility. Software is a tool. It 
should be made to make things *possible*, not to make things *right* 
from the start. The beauty of tools is that they're used for things that 
their creators didn't think at start.


This:


"The -maxwarn option can be used to override warnings printed by grompp
that otherwise halt output. In some cases, warnings are harmless, but
usually are not. The user is advised to carefully interpret the output
messages before attempting to bypass them with this option."

If that sounds agreeable, I'll put in an enhancement request.


is good because it *tells* the user that something serious is happening. 
But removing or hiding, is a no-no. More information, the better.


But it seems we agree, so thanks a lot!

m.

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Re: [gmx-users] trjconv with multiple chains

[ms]

On 07/01/11 02:17, yuanyuan wang wrote:

dear all,
  I am doing a simulation that have many chains in a box , and I can 
find a center for them after serval tries.
  I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , 
-ur compact, -center , -box to got bigger box, and -boxcenter, -fit ..
  still some chain cannot convert into box. them jump from one box to 
another ,
  is there any ways that they not jump to another box?
  thanks a lot.



If they do cluster together fast (like mine), the solution I found -with 
the help of Justin Lemkul, if I remember correctly- was to use trjconv 
for simply centering on one of the chains. This way the aggregate, once 
formed, stayed in the center.


If they just diffuse, I suspect there's nothing you can do: you have 
stuff diffusing in a periodic system, and WYSIWYG.


m.

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Re: [gmx-users] justin

[ms]

On 07/01/11 17:00, mustafa bilsel wrote:

Justin,

Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH.

Nothing changed. I suggest you to try it by yourself.
Don't try to remind people the help rules.
JUST HELP OR DONOT HELP.


We're not at your orders and shouting at people who try to help you is 
unbelievably rude. Therefore, in any case, with you I'll choose the 
second option. Bye, you're going in my spam folder.


m.



mustafa


This topology defines the [moleculetype] name as "Methanol," which is the
name
that needs to be used in the [molecules] directive below.  But then, too,
you're
not using the same residue name either (MTH instead of MeOH), so it is still
not
possible to say what's going wrong.

-Justin





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[gmx-users] Geometry-dependent (non-spherically symmetric) potentials

[ms]

Hi,

While I understand that all non-bonded gmx potential shapes are intended 
to be spherically symmetric, for a project of mine it would be helpful 
to be able to have a non-bonded pair potential which is 
geometry-dependent (that is, depending on the angle between 3 atoms).


Has anything -official or unofficial- of this kind ever been attempted 
on Gromacs and, if yes, are there code examples to look at?


Any kind of advice is welcome!

thanks,
Massimo

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Re: [gmx-users] energy minimization of a charged system in vacuum

[ms]

On 29/01/11 05:08, Matt Chan wrote:

Perfect. This is great reading.

Thanks for the pointers Mark.

Matt

On 01/28/2011 06:50 PM, Mark Abraham wrote:

On 29/01/2011 9:57 AM, Matthew Chan wrote:

Hi,

I'm a first time GROMACS user. I've got 2 questions, which I'll ask
in separate emails. The first is about running EM on a charged
protein in vacuum.

I'm presently walking through some of the tutorials and trying to
simplify them for my purposes. One is the energy minimization of the
1AKI lysozyme protein. I would like to minimize this protein in
vacuum instead of solution as the tutorial demonstrates. Since the
genion program replaces water molecules with ions to balance the
charge of the system and there's no water, I'm having trouble running
the simulation with a neutral system.

My question is what effect does running a simulation with a charged
system have? I recall reading that something related to PME
calculations assumes the system is neutral, but it did not specify
whether it was referring to MD or EM. From the mailing list, I have
only been able to determine that running a charged system in solution
makes no sense biologically.


Some threads elsewhere cover these issues:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html
http://archive.ambermd.org/200712/0223.html

Mark



Since I have exactly the same needs (charged system in vacuum) I jump in...

In http://www.gromacs.org/Documentation/Errors
it says:

Note for PME users: It is possible to use a uniform neutralizing 
background charge in PME to compensate for a system with a net 
background charge. There is probably nothing wrong with this in 
principle, because the uniform charge will not perturb the dynamics.


From the reading above, it seems that namd/amber implementations 
already *implicitly* use this kind of compensation by ignoring terms in 
the summation. Is it the same for GROMACS?


thanks,
M.

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Re: [gmx-users] energy minimization of a charged system in vacuum

[ms]

On 30/01/11 15:41, David van der Spoel wrote:


My question is what effect does running a simulation with a charged
system have? I recall reading that something related to PME
calculations assumes the system is neutral, but it did not specify
whether it was referring to MD or EM. From the mailing list, I have
only been able to determine that running a charged system in solution
makes no sense biologically.


Some threads elsewhere cover these issues:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html
http://archive.ambermd.org/200712/0223.html

Mark



Since I have exactly the same needs (charged system in vacuum) I jump
in...

In http://www.gromacs.org/Documentation/Errors
it says:

Note for PME users: It is possible to use a uniform neutralizing
background charge in PME to compensate for a system with a net
background charge. There is probably nothing wrong with this in
principle, because the uniform charge will not perturb the dynamics.


I'd like to comment that, this is tricky business. If your charges are
spread out homogeneously it may be OK, but in practice this is often not
the case (e.g. side chains on a protein). One should try to avoid this
if at all possible.


Oh, this is very bad news. Could you elaborate on that? (I have a CG 
model where this would be badly needed).


Can spreading neutralizing charges along the other chain atoms be a 
viable alternative for enough atoms and enough low charge? (e.g. if I 
have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?)



From the reading above, it seems that namd/amber implementations
already *implicitly* use this kind of compensation by ignoring terms in
the summation. Is it the same for GROMACS?

thanks,
M.


Gromacs does not ignore any terms in the simulations if I am not
mistaken. It also computes PME at every step in contrast to NAMD (don't
know about Amber).


Thanks.
m.

--
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http://devicerandom.org
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Re: [gmx-users] mailing list search

[ms]

Rossen Apostolov ha scritto:
> Hi,
> 
> I made some updates and incorrectly changed the permissions.
> You should be able to search now even without logging in.
> 

I jump in this thread to ask: I've notice that there are a huge amount
of broken links in the new Gromacs pages. This is bad for me since I am
just beginning to learn Gromacs!

Google cache and the PDF manual are my friends, but any hint on where to
retrieve the pages that are still linked as being on the old wiki is
appreciated.

thanks,
M.

> Rossen
> 
> Sun Joo Lee wrote:
>> Hello
>>
>> I have been trying to search the mailing list after I logged in to the
>> new gromacs website. 
>> But I do not get any searched results but "This page is restricted."
>> comment.
>>
>> Could anyone tell me what the problem might be? 




>>
>> Thank you
>> Sunjoo 
>> 
>>
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Re: [gmx-users] mailing list search

[ms]

Justin A. Lemkul ha scritto:
> 
> 
> ms wrote:
>> Rossen Apostolov ha scritto:
>>> Hi,
>>>
>>> I made some updates and incorrectly changed the permissions.
>>> You should be able to search now even without logging in.
>>>
>>
>> I jump in this thread to ask: I've notice that there are a huge amount
>> of broken links in the new Gromacs pages. This is bad for me since I am
>> just beginning to learn Gromacs!
>>
>> Google cache and the PDF manual are my friends, but any hint on where to
>> retrieve the pages that are still linked as being on the old wiki is
>> appreciated.
>>
> 
> The old wiki has been taken down.  You can search the Gromacs site (not
> the mailing list) for relevant content, until all the links are
> working.  There has been some discussion about this lately; it will be a
> very time-consuming task.

Searching I tried, but it seems it led almost always to blank pages. I
will try now, maybe it was the same bug of the mailing list search.

Thanks.

m.

> 
> -Justin
> 
>> thanks,
>> M.
>>
>>> Rossen
>>>
>>> Sun Joo Lee wrote:
>>>> Hello
>>>>
>>>> I have been trying to search the mailing list after I logged in to the
>>>> new gromacs website. But I do not get any searched results but "This
>>>> page is restricted."
>>>> comment.
>>>>
>>>> Could anyone tell me what the problem might be? 
>>
>>
>>
>>
>>>> Thank you
>>>> Sunjoo
>>>> 
>>>>
>>>>
>>>> ___
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> 

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Re: [gmx-users] mailing list search

[ms]

Justin A. Lemkul ha scritto:
 Google cache and the PDF manual are my friends, but any hint on
 where to
 retrieve the pages that are still linked as being on the old wiki is
 appreciated.

>>> The old wiki has been taken down.  You can search the Gromacs site (not
>>> the mailing list) for relevant content, until all the links are
>>> working.  There has been some discussion about this lately; it will be a
>>> very time-consuming task.
>>
>> Searching I tried, but it seems it led almost always to blank pages. I
>> will try now, maybe it was the same bug of the mailing list search.
>>
> 
> Some pages simply may not exist, depending on what you're looking for.

Ouch.
Well, I'd like to help with fixing the links whenever I find a broken
one, but it seems I can't edit. :)

m.
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Re: [gmx-users] mailing list search

[ms]

Justin A. Lemkul ha scritto:
> ms wrote:
>> Justin A. Lemkul ha scritto:
>>>>>> Google cache and the PDF manual are my friends, but any hint on
>>>>>> where to
>>>>>> retrieve the pages that are still linked as being on the old wiki is
>>>>>> appreciated.
>>>>>>
>>>>> The old wiki has been taken down.  You can search the Gromacs site
>>>>> (not
>>>>> the mailing list) for relevant content, until all the links are
>>>>> working.  There has been some discussion about this lately; it will
>>>>> be a
>>>>> very time-consuming task.
>>>> Searching I tried, but it seems it led almost always to blank pages. I
>>>> will try now, maybe it was the same bug of the mailing list search.
>>>>
>>> Some pages simply may not exist, depending on what you're looking for.
>>
>> Ouch.
>> Well, I'd like to help with fixing the links whenever I find a broken
>> one, but it seems I can't edit. :)
>>
> 
> You have to register as a contributer and log in (top right of the
> Gromacs page).

I registered yesterday and I am logged in, but perhaps I am not
registered "as contributor"...

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Re: [gmx-users] mailing list search

[ms]

Justin A. Lemkul ha scritto:
>>> The old wiki has been taken down.  You can search the Gromacs site
>>> (not
>>> the mailing list) for relevant content, until all the links are
>>> working.  There has been some discussion about this lately; it will
>>> be a
>>> very time-consuming task.
>> Searching I tried, but it seems it led almost always to blank
>> pages. I
>> will try now, maybe it was the same bug of the mailing list search.
>>
> Some pages simply may not exist, depending on what you're looking for.
 Ouch.
 Well, I'd like to help with fixing the links whenever I find a broken
 one, but it seems I can't edit. :)

>>> You have to register as a contributer and log in (top right of the
>>> Gromacs page).
>>
>> I registered yesterday and I am logged in, but perhaps I am not
>> registered "as contributor"...
>>
>>
> 
> All I meant was to create an account.  What page are you attempting to
> modify? Some pages cannot be modified except by administrators.

Well, I'd like to tell you, but it seems every page now is failing with

"Site settings could not be loaded

We were unable to locate the API to request site settings. Please see
below for debugging information.

HTTP Response Status Code: 0"

I guess I'll wait for the website situation to settle by reading the
manual... :)

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Re: [gmx-users] mailing list search

[ms]

Justin A. Lemkul ha scritto:

>> Well, I'd like to help with fixing the links whenever I find a broken
>> one, but it seems I can't edit. :)
>>
> You have to register as a contributer and log in (top right of the
> Gromacs page).
 I registered yesterday and I am logged in, but perhaps I am not
 registered "as contributor"...


>>> All I meant was to create an account.  What page are you attempting to
>>> modify? Some pages cannot be modified except by administrators.
>>
>> Well, I'd like to tell you, but it seems every page now is failing with
>>
>> "Site settings could not be loaded
>>
>> We were unable to locate the API to request site settings. Please see
>> below for debugging information.
>>
>> HTTP Response Status Code: 0"
>>
> 
> What site are you trying to load?  I'm logged in right now (fixing a few
> things), so it appears the website is working quite well right now.
> 
> -Justin

Probably a hiccup, now it works again.
Anyway, example of pages I can't edit... I'd say "all of them", but:

http://www.gromacs.org/Documentation/File_Formats/Topology_(.tpr)_File
http://www.gromacs.org/Documentation/Terminology/Average_Structure
http://www.gromacs.org/Documentation/File_Formats/.pdb_File

are just three I have tabs opened.

Funnily enough, I can't even edit *my* userpage:
http://www.gromacs.org/User:devicerandom

m.
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Re: [gmx-users] mailing list search

[ms]

Rossen Apostolov ha scritto:
> Hi,
>> I registered yesterday and I am logged in, but perhaps I am not
>> registered "as contributor"...
>>   
> I added you as a contributor. Thanks for offering to help!
> 
> New users are only "viewers" by default to avoid giving instant write
> permissions to everyone. People who would like to contribute should send
> me a mail and I'll change their role. There is a note about that in bold
> on the front page.

Ops. Apologize for my distraction, my brain missed it.

If you feel like that, I'd like to correct links whenever I find them. :)

m.
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[gmx-users] Tips and tricks to make your own coarse-grained model?

[ms]

Hi,

First of all, I am new to Gromacs and quite new to the MD field (I had a
read of the Daan-Frenkel book and played very little with custom CG
models - I used to be an experimental guy), so please bear with me if
questions happen to be naive.

My aim is to re-implement a formerly standalone CG model by mean of gmx.
It seems that gmx is well suited to the task; however I understand that
there is an incredible number of pitfalls where a newbie fall in.

I am currently reading and re-reading the manual, looking at the online
docs and tutorials. But most of information, understandably, refer to
all-atom modeling and there is little on how to build your own model on gmx.

Maybe my googling skills are not as good as once they were -in this case
can anyone point me to any page where this kind of task is documented?

If such a page there isn't (and even if there is), I would appreciate a
lot if anyone of you can share your wisdom on best practices, pitfalls,
things to know etc. before diving head-on in such an endeavour.

Thanks a lot!

Massimo
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Re: [gmx-users] Tips and tricks to make your own coarse-grained model?

[ms]

Justin A. Lemkul ha scritto:
>> My aim is to re-implement a formerly standalone CG model by mean of gmx.
>> It seems that gmx is well suited to the task; however I understand that
>> there is an incredible number of pitfalls where a newbie fall in.
>>
>> I am currently reading and re-reading the manual, looking at the online
>> docs and tutorials. But most of information, understandably, refer to
>> all-atom modeling and there is little on how to build your own model
>> on gmx.
>>
>> Maybe my googling skills are not as good as once they were -in this case
>> can anyone point me to any page where this kind of task is documented?
>>
>> If such a page there isn't (and even if there is), I would appreciate a
>> lot if anyone of you can share your wisdom on best practices, pitfalls,
>> things to know etc. before diving head-on in such an endeavour.
>>
> 
> So, to clarify, this is an already-existing CG model that you simply
> want to use for simulations in Gromacs?  It is then rather easy.  You
> need to define all appropriate force field files (nb.itp, bon.itp, .atp,
> etc), and perhaps .rtp files if you can also come up with a way to
> define an appropriate CG input for pdb2gmx.

Yes. I know the specs of the cg model, and I want to re-implement it
within gromacs. Actually it is a class of related models. I'd start from
a very minimal one and then improve gradually.

I understand I have to define all appropriate FF files, but I wonder
what is the best way to do it, what documentation to learn by heart,
what sanity checks... You make me optimist in saying "it is rather easy"
, but science is always full of traps, especially for the newcomer...

thanks!
m.
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[gmx-users] What is best way to get multiple chains?

[ms]

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx
- Used editconf to create translated copies
- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?

Thanks a lot,
Massimo
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Re: [gmx-users] What is best way to get multiple chains?

[ms]

Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> I am a gmx newbie, so please don't bite too much! :)
>>
>> Learning gmx, I am experimenting with simulations with multiple
>> identical small chains. What I did was:
>>
>> - I generated the peptides with pymol
>> - Generated a .gro with pdb2gmx
> 
> This step is "generating a molecular topology". You don't need a .gro -
> it's just a regularized coordinate file produced as a side-effect.

Very much right. Thanks.

>> - Used editconf to create translated copies
> 
> Try genconf to do the replication. That should remove much of the manual
> labour. You would still probably need to edit in the chain IDs yourself,
> but that's easy work with a script or good editor.

Thanks!

>> - Stitching them together and creating the complete file, adjusting
>> numbers etc. manually
>>
>> It worked well, but the chains are not recognized as *different* chains
>> -which could be useful. Documentation says I should use another format
>> like the pdb, but it is a bit sparse on the subject. I think I can use
>> pdb instead of gro if needed, but does this also work when creating
>> boxes etc.? Isn't there a way to get chain identifiers in a gro file?
>> What is best practice?
> 
> What do you want the chain identifiers for? I'm not aware of a
> post-pdb2gmx purpose that they might serve.

This is where my naivety probably enters in: Analysis programs work on
groups. If several chains are defined, can each of these count as a
group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
is to get analysis for each chain in my system. What is best practice
for that / where should I look in the docs?

> If your system is N identical peptides in a solvent, then best practice
> for generating a complete .top is to generate one for a single peptide
> in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a
> coordinate file which contains the N peptides' coordinates followed by
> all the solvent (e.g. genconf - genbox). Then edit the [ molecules ]
> section of the original .top to match. Other solutions are possible, but
> require more involved use of pdb2gmx, and might indeed want chain IDs.

Uh, thanks. Not sure to have understood all of it, but I will do my
homework before coming back :)

m.
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Re: [gmx-users] What is best way to get multiple chains?

[ms]

Mark Abraham ha scritto:
> ms wrote:
>> Mark Abraham ha scritto:
>>> What do you want the chain identifiers for? I'm not aware of a
>>> post-pdb2gmx purpose that they might serve.
>>
>> This is where my naivety probably enters in: Analysis programs work on
>> groups. If several chains are defined, can each of these count as a
>> group? Indeed, chapter 8 doesn't explicitly say so, but... My intention
>> is to get analysis for each chain in my system. What is best practice
>> for that / where should I look in the docs?
> 
> make_ndx is the tool for generating such groups. If you read make_ndx -h
> you'll see it does indeed let you create groups based around chain IDs,
> but that'd (at least) require supplying it with a coordinate file that
> has chain IDs. You could do that, but doing the house-keeping to assign
> those IDs is tricky, and with PDB you're probably limited by 26 letters.
> make_ndx will also let you create a group according to a range of atomic
> numbers "a 1-10" or residue numbers "r 1-10". This avoids needing to
> preserve/create chain IDs. Since you only need to create index groups
> once for a given coordinate file, that's not too onerous. If you will
> have lots of simulations with different numbers of such groups then you
> might write a script to automate that... see
> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
> 

Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do
you mind if I later I try to update the "multiple chains" wiki page
based on your advices?

>>> If your system is N identical peptides in a solvent, then best practice
>>> for generating a complete .top is to generate one for a single peptide
>>> in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a
>>> coordinate file which contains the N peptides' coordinates followed by
>>> all the solvent (e.g. genconf - genbox). Then edit the [ molecules ]
>>> section of the original .top to match. Other solutions are possible, but
>>> require more involved use of pdb2gmx, and might indeed want chain IDs.
>>
>> Uh, thanks. Not sure to have understood all of it, but I will do my
>> homework before coming back :)
> 
> Sure. Doing some "irrelevant" tutorial material can be useful
> introductions to the workflows. Regard;ess, the learning curve can be
> steep for all computational chemistry software. Unfortunately no
> beginner these days seems to want to come in and just do
> protein-in-water :-) That makes their life hard.

Yep, unfortunately that's kinda not simply "protein-in-water". I am
trying to understand all pieces I need very slowly, step-by-step. And I
guess you will hear my cries often in this ML :)

Thanks again,

m.
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[gmx-users] how to mimick explicit hydrogen bonding

[ms]

Hi,

I need to implement a FF which includes directional hydrogen bonding. It
seems however, to my understanding, that Gromacs has no simple way to
include an explicitly directional contribution. All I can find is that,
in standard force fields, h-bond terms are implicitly described by
coulombic and vdw interactions, but I am a bit puzzled by how these
terms are combined to give a directional interaction.

Can anyone give me hints on how to describe a directional
hydrogen-bond-like interaction?

thanks!

m.
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Re: [gmx-users] how to mimick explicit hydrogen bonding

[ms]

Hi Mark,

Thanks for your answer.

Mark Abraham ha scritto:
> There's nothing directional about the physics of a hydrogen bond, unless
> your model makes it so. There'd be nothing intrinsically valid or
> invalid with that either, so long as you parameterized the force field
> under that assumption. If using rigid water models and/or other atomic
> constraints where H-bonded atoms can't have a geometric distortion, I
> suppose such a model might be necessary. It's still far from clear that
> H-bonding is sufficiently different from other electrostatic
> interactions to warrant special treatment (and thus reparameterization
> of charges).

Ok, the problem is that I want to re-implement a quite minimal
coarse-grained FF (so no explicit solvent etc.) and a directional
interaction would be useful.

>> Can anyone give me hints on how to describe a directional
>> hydrogen-bond-like interaction?
> 
> You would not achieve this in GROMACS without code modification. A
> special non-bonded list for H-bonded water (and maybe H-bonded
> non-water) that didn't call the standard water inner loops would be
> required.

I see. I asked because I think I've read that there were force fields
with explicit hydrogen bond treatment (some CHARMM?) that were imported
into Gromacs, and I thought there was some clever hack to get it working
-but I guess that it is not the case.

Thanks!
m.
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Re: [gmx-users] how to mimick explicit hydrogen bonding

[ms]

Mark Abraham ha scritto:
> ms wrote:
>> Ok, the problem is that I want to re-implement a quite minimal
>> coarse-grained FF (so no explicit solvent etc.) and a directional
>> interaction would be useful.
> 
> Well you should consider alternative software, then.

I see. I wonder if patching gmx to do that is possible/difficult,
however (I'm not confident at all in doing that, but I know closely
people who are).

> IIRC, CHARMM did have explicit H-bond models ages ago, but (again IIRC)
> they're not in the modern versions and not in the upcoming GROMACS port.

Ok, thanks for clarifying!

Thanks,
M.
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[gmx-users] Quick question about g_mindist

[ms]

Hi,

I am using g_mindist to see how close get C-alphas to each other in my
chains. What I do is selecting C-alpha two times when prompted. I have
only a quick question, just to be sure: The script doesn't take into
account the distance between *neighbouring C-alpha*, isn't it?

thanks!

m.

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Re: [gmx-users] Quick question about g_mindist

[ms]

Hi Justin,
thanks for your answer

Justin A. Lemkul ha scritto:
>> I am using g_mindist to see how close get C-alphas to each other in my
>> chains. What I do is selecting C-alpha two times when prompted. I have
>> only a quick question, just to be sure: The script doesn't take into
>> account the distance between *neighbouring C-alpha*, isn't it?
>>
> 
> I don't see why they wouldn't be.  I suppose you'd have to look into the
> code to be sure.  But if you choose C-alpha for analysis, then I would
> imagine all of those atoms are going to be considered.
> 
> If there are specific interactions you are looking for, create specific
> index groups for those residues, otherwise I don't know if you're going
> to gain much from this analysis, because the minimum distance within a
> protein may always occur between two specific atoms, oscillating about a
> certain value.

I am not looking for specific interaction now, I am only interested in
how the chain self-avoids itself in general.

However I guess from your above comment that g_mindist cannot read my
mind as I hoped :)

thanks!
m.
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[gmx-users] Density histogram in Ramachandran plot

[ms]

Hi,

I wonder if there is an easy way I am missing to get a density histogram
from the Ramachandran plot over a trajectory as outputted by g_rama. All
I see are big, uniform black blobs and they're not helpful, because with
tons of data points a density plot would be much more informative. Thanks!

m.
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[gmx-users] Tabulated non-bonded potential

[ms]

Hi,

I would like to understand a basic question about the usage of tabulated
potential for non-bonded interaction. If I use an arbitrary function and
I write a table for it, is the functional shape then applied to *all* my
atoms, or can I specify which ones use the tabulated potential -and how?

Thanks,
M.
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Re: [gmx-users] Tabulated non-bonded potential

[ms]

Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> I would like to understand a basic question about the usage of tabulated
>> potential for non-bonded interaction. If I use an arbitrary function and
>> I write a table for it, is the functional shape then applied to *all* my
>> atoms, or can I specify which ones use the tabulated potential -and how?
> 
> Use energygrp_table in the .mdp file. See manual section 7.3


*slap on my head*
Thanks, I missed it. I was looking in the Chapters 4 and 5 and finding
nothing I was confused.

m.

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Re: [gmx-users] Tabulated non-bonded potential

[ms]

I have a further question about tabulated non-bonded potentials.

The manual (6.7.2) says:
"It is also possible to combine a standard Coulomb with a modified LJ
potential... The table file must always contain the 7 columns however,
and meaningful data (i.e. not zeroes) must be entered in all columns".

What's wrong with the zeroes? Is any other number valid (e.g. a column
of 1's?) What kind of "meaningful data" am I going to put in, if I will
not use them?

Thanks!

m.
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[gmx-users] What is the current wisdom on energy leak?

[ms]

Dear Gromacs users,

I am a little new fellow in this community, and many things still I
don't know.

I am trying to parametrize a coarse-grained FF for polymer simulations,
without solvent. A collegue of mine advised me, just to be sure, to
check for possible energy leak artefacts. To do that he told me that I
should run a simulation with no thermal coupling and check the energy
conservation. He told me that in such case, in a well-behaved system,
"dE/E<10-4, 10-5" (where dE is the RMSD?).

By playing with that indeed I found that, as expected, using pme-switch
and shift for Coulombd and VdW respectively helps a lot (with respect to
cut-offs), but even increasing LINCS, decreasing neighbour search time
etc. my ratio doesn't go below 2E-3. I wonder however if there are also
possibly poor minimization effects in that -it seems that it minimizes
correctly, but...

My problem however is that apart from that informal advice I can find
very little practical on the subject. The only clear thing I can find on
the net is a Van der Spoel students tutorial which says:

https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html#mozTocId961213

"Conservation of energy can be monitored by checking the ratio of the
fluctuations in Total energy and the Kinetic Energy. For a well behaved
system the ratio R:
R = Δ Etot/Δ Ekin
should be less than 0.05."

but it doesn't specify, as far as I can see, the conditions in which
this is a good ratio (solvent, no solvent, which thermostat, etc.).

Has anyone advices for bibliography or some general practical wisdom on
this problem?

Thanks a lot,
Massimo
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[gmx-users] Tabulated potentials make newbies crazy

[ms]

Hi,

I am really having a hard time figuring out how to use tabulated
potentials correctly.

In general, the information on how to use tables is sparse and scattered
in several points of the manual (ch.5, ch.7, ch.6.7...) -I hope to write
a short howto in the wiki once I get this working, but now I really
don't know what to do.

This is the story, sorry if it is long, but...:

My problem is conceptually simple:I want to use a tabulated potential
for the Calpha in my protein chain,to build a CG model.

I want the Calpha to use the tabulated potential,both between themselves
and with other atoms, and I want other atoms to behave between
themselves just as before (or at least as possible as close as before,
at least for now).

I first tried therefore to put C-alpha in the energy groups, called the
table table_C-alpha_C-alpha.xvg, vdw=user , and there it complains
because one atom cannot belong to two energy groups (C-alpha and
Protein) at the same time.

Just to try, therefore, I removed all occurences of energy groups in a
.ndx files, except for system and C-alpha (I have no solvent). And there
it complains that atoms belong to different energy groups, but belong to
the same charge group.

I understand therefore that energy groups and charge groups must be
identically defined.

Anyway, just for the sake of learning how to get gmx use a tabulated
potential, I apply the tabulated potential to all the peptide chain,
(and I rename the table table_protein_protein.xvg). At this point, it
stops asking me for a "table.xvg" file. I realize that it probably wants
to know how to define other non bonded interaction. Since there is only
the protein, I rename the table_protein_protein.xvg as table.xvg and retry.

And now I cry because mdrun doesn't start, telling me:

   Fatal error:
   Out of range force value 2.44081e+41 in file 'table.xvg'

The "out of range force value" error does not appear at all on google. I
understand it's "kinda high" - but it's a very steep repulsion and so it
is naturally like that at distances close to 0.

Now, my questions are:
- What is the accepted range of values in tables?
- How do I define a steep repulsion potential correctly?
- Is there a way to define a table for specific atoms in a chain,
leaving the other atoms using the standard VdW potential? I guess it
requires splitting the chain in two energy groups, but I don't
understand if it a)makes sense/creates problems b)how to deal with the
fact that the chain should be a single charge group.

Thanks to everyone!
m.
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Re: [gmx-users] Tabulated potentials make newbies crazy

[ms]

Dear Mark,

First of all, thanks for your patient and thorough reply!

Mark Abraham ha scritto:
> Yeah, that's an unfortunate fact of life. The manual can't be organized
> so that everybody finds all the information they want in one location
> with the detail they need right now. Using tabulated potentials is an
> advanced feature and if the user needs to search the manual diligently
> to find the information, that's probably good for them in the long run.
> There's a good table of contents, index and some cross references, and
> text-searching is also available...

Yes, that's what I am doing now but it seems I am not good enough at it
:) .Don't get me wrong, the manual is truly, amazingly, incredibly good
-but probably a wiki page on the subject could help people tie the
strings together more easily. When I'll get all of this correct I wish
to draft one so that you can correct it.

>> Just to try, therefore, I removed all occurences of energy groups in a
>> .ndx files, except for system and C-alpha (I have no solvent). And there
>> it complains that atoms belong to different energy groups, but belong to
>> the same charge group.
>>
>> I understand therefore that energy groups and charge groups must be
>> identically defined.
> 
> No. You should read in the manual about groups - sections 3.3 and 8.1.1

I've read them -read both of them *now* again, actually- and still I see
no mention of charge groups in the paragraph you linked -apart perhaps
for this sentence in 3.3: " This is done separately for Lennard-Jones
and Coulomb terms." -They are described in 3.4 ,and also in 4.6 for
example, but I find no information on how they're differently described
with respect to energy groups. It tells me they're described in the
topology, but nothing more. If I look at my topology, I find no charge
group definition.

The problem is that since I have a single molecule now, and the single
molecule must be neutral, so it must be all a single charge group
("Therefore we have to keep groups of atoms with total charge 0
together. These groups are called charge groups.", 4.6.2).

> Get the energy group stuff working before you worry about providing user
> tables. Divide-and-conquer makes troubleshooting much easier.

Right, thanks...

>> Anyway, just for the sake of learning how to get gmx use a tabulated
>> potential, I apply the tabulated potential to all the peptide chain,
>> (and I rename the table table_protein_protein.xvg). At this point, it
>> stops asking me for a "table.xvg" file. I realize that it probably wants
>> to know how to define other non bonded interaction. Since there is only
>> the protein, I rename the table_protein_protein.xvg as table.xvg and
>> retry.
> 
> Group names are probably case sensitive, so your filename must match
> your group names... the above doesn't look right.

The group name was in lower case, that is why I called it in lower case
(for C-alpha I used upper case as in the group name). It recognized it
somehow. But thanks for pointing it, I'll retry.

>> And now I cry because mdrun doesn't start, telling me:
>>
>>Fatal error:
>>Out of range force value 2.44081e+41 in file 'table.xvg'
>>
>> The "out of range force value" error does not appear at all on google. I
>> understand it's "kinda high" - but it's a very steep repulsion and so it
>> is naturally like that at distances close to 0.
> 
> That looks like a bug with mdrun trying to read from a non-existent
> file. It is always useful to provide your exact command lines, rather
> than leave us to infer from text.

Sorry. This is from the script I use to launch the job on the cluster
(it is not, however, a parallel job):

mdrun -v -s $STARTDIR/fullmd_xab10_01.tpr -o $STARTDIR/xab10_traj01.trr
-x $STARTDIR/xab10_traj01.xtc -c $STARTDIR/xab10_final01.gro -e
$STARTDIR/xab10_ener01.edr 2>&1 > $STARTDIR/output_20091127_xab01.txt

Now however, thanks to your suggestion, I checked my table and I found
that I defined a derivative (the 2.44081e+41 value indeed) for r=0.

Adjusting that (putting it to 0, since r=0 makes little sense), it
complains for the next, huge value, at r=0.002. The values it complains
about are always real ones in the table, so it finds it and reads it. I
can now regenerate it however such that it stays constant when energy is
larger, say, than 50.000. This is probably the least problem, but some
advice on it, just for the sake of completeness, could be nice.

>> Now, my questions are:
>> - What is the accepted range of values in tables?
> 
> I don't think this is the problem.

It is the least problem probably, given my confusion on energy-charge
groups, but it seems it is too...

>> - How do I define a steep repulsion potential correctly?
> 
> It's terse, but manual 6.7 seems to have the necessary information.

6.7 is one of the references I am obviously using, but it gives only
general (even if essential!!) information, nothing speficic on "good" or
"bad" potential shapes/values. But probably that's the least prob

Re: [gmx-users] Tabulated potentials make newbies crazy

[ms]

Mark Abraham ha scritto:
 > Sorry, I was a bit incomplete last night. Charge groups are the
> fundamental unit for neighbour-searching (3.4.2) to construct lists of
> charge groups for nonbonded interactions, which determine lists of
> atom-atom interactions. However, the nonbonded interactions are
> evaluated as nested sums, first over energy groups. So for energy groups
> of Protein and SOL, the neighbour search finds all pairs of charge
> groups that are both Protein and inside the cutoffs, and lists them.
> Then all Protein-SOL similarly, then all SOL-SOL. This requires that the
> energy groups be a union of only complete charge groups (and I am not
> aware that this is spelled out anywhere in the manual!). So for energy
> groups of Calpha, Rest_of_Protein and SOL, it would be necessary to use
> an individual charge group for each Calpha. This would usually mean it
> has a net non-integral charge that is equal in magnitude of the charge
> of the group from which it is taken. It is well known that small charge
> groups of non-integral charge can then wander back and forth across
> cut-off boundaries and generate artefacts.

Ok, thanks for the clarification. This doesn't suggest a trivial
solution to the problem, quite the opposite: I understood correctly that
charge groups must be neutral, and this is impossible to do if we put
each C-alpha as a charge group.

I can coarse the thing further -that's quite the plan, actually- and
eliminate electrostatics, but I hoped to have a look at what happens
with the new potential and getting it right, before going so far.

So, even if the following:
>> The problem is that since I have a single molecule now, and the single
>> molecule must be neutral, so it must be all a single charge group
>> ("Therefore we have to keep groups of atoms with total charge 0
>> together. These groups are called charge groups.", 4.6.2).

is not entirely correct, it is indeed correct that charge groups
*should* be neutral. Isn't it?

> If you're running in single precision, that precision cannot represent
> values as large as 10^41. Since in any simulation (but particularly
> coarse-grained one) non-bonded atoms aren't going to get this close, the
> values are next to irrelevant. Just choose 10^38 for anything larger
> than that.

Right, it is probably precision problem. Thanks.

 Now, my questions are:
 - What is the accepted range of values in tables?
>>> I don't think this is the problem.
>>
>> It is the least problem probably, given my confusion on energy-charge
>> groups, but it seems it is too...
>>
 - How do I define a steep repulsion potential correctly?
>>> It's terse, but manual 6.7 seems to have the necessary information.
>>
>> 6.7 is one of the references I am obviously using, but it gives only
>> general (even if essential!!) information, nothing speficic on "good" or
>> "bad" potential shapes/values. But probably that's the least problem :)
> 
> Knowing a sensible shape is your problem, if you're choosing to
> unbalance the force field by changing one of the contributing potentials...

I meant "sensible" in the meaning of "can be interpolated more or less
faithfully / will be calculated with more or less artefacts" -of course
if it makes sense in the model is my problem...

> Best of luck!

It seems to be in scarce supply these days (just lost a fellowship, argh).

Cheers,
m.
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[gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?

[ms]

Hi,

As per the title. I need to understand what is the difference to help
myself debug my inane efforts at CG parametrization. LJ(1-4) I think is
clear (non bonded, non-coulombic interactions between 1-4 pairs
described in the topology), but about the rest?

thanks!

m.

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Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?

[ms]

Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> As per the title. I need to understand what is the difference to help
>> myself debug my inane efforts at CG parametrization. LJ(1-4) I think is
>> clear (non bonded, non-coulombic interactions between 1-4 pairs
>> described in the topology), but about the rest?
> 
> See manual 4.6.3

Seen it, still don't get it :)

m.

> Mark

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Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?

[ms]

Justin A. Lemkul ha scritto:
 As per the title. I need to understand what is the difference to help
 myself debug my inane efforts at CG parametrization. LJ(1-4) I think is
 clear (non bonded, non-coulombic interactions between 1-4 pairs
 described in the topology), but about the rest?
>>> See manual 4.6.3
>>
>> Seen it, still don't get it :)
>>
> 
> A good reason to search the mailing list...
> 
> http://lists.gromacs.org/pipermail/gmx-users/2007-December/031264.html


Uh, thanks! I always google the ML before asking, but my googling skills
are evidently not as good as I thought. Thanks!
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Re: [gmx-users] How to increase nodes in mdrun option

[ms]

Mahendran E ha scritto:
> hi all
> 
> while running gromacs in parallel environment
> 
> i am getting the following command,
> 
> the command i used is
> 
> mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s
> fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr
> 
>
> error:
> 
> 
> 
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: domdec.c, line: 5873
> 
> Fatal error:
> There is no domain decomposition for 5 nodes that is compatible with the
> given box and a minimum cell size of 1.095 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> settings
> Look in the log file for details on the domain decomposition
> ---
> 
> "Everybody Wants to Be Naked and Famous" (Tricky)
> 
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 0 out of 5
> 
> gcq#130: "Everybody Wants to Be Naked and Famous" (Tricky)
> 
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_16810:  p4_error: : -1
> p4_error: latest msg from perror: No such file or directory
> 
> 
> how to increase the nodes in mdrun option

Increasing the number after mpirun -np , I'd say.

m.
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Re: [gmx-users] GRACE

[ms]

pawan raghav ha scritto:
> Hi,
> 
> Please tell me how to install GRACE source files to execute xmgrace command
> to visualize 2D graph. I am unable to installed it as read from tutorial.
> please help me as I am in need.
> 

Contact the xmgrace mailing list.

m.
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