date:20120316

Re: [gmx-users] Generation of the Distance Restraints

2012-03-16 Thread James Starlight

> 2) Also I've found that there is more simple way to define restraines
> based on the BONDS enty in the topology file. Could you provide me with the
> more information about this simpler way ?
>
>
> Simpler, but not a restraint to within a region. The manual section we are
> discussing links you to the available documentation elsewhere in the
> manual. I don't have the time to help with every interpretation question
> you might have.
>
> Mark
>
> Mark,


In more details I want to generate network of disres for all helices
H-bonds. So I want to restraint H-bond distance between i and i+4 atoms of
the backbone.

What is the simplest way to do such task? I think that the ussage of
genrestr -disre could be useful for such generation of the complex disres
because of the size of my protein. But how I could define the restrained
atoms (i, i+4 atoms ) ? In the make_ndx options I didnt find the most
trivial sollution of the such choise. So the only sollution is to define
each I and I+4 atoms of the backbone manualy, isnt it ?

James
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Re: [gmx-users] Generation of the Distance Restraints

2012-03-16 Thread Mark Abraham


On 16/03/2012 6:39 PM, James Starlight wrote:



2) Also I've found that there is more simple way to define
restraines based on the BONDS enty in the topology file. Could
you provide me with the more information about this simpler way ?


Simpler, but not a restraint to within a region. The manual
section we are discussing links you to the available documentation
elsewhere in the manual. I don't have the time to help with every
interpretation question you might have.

Mark

Mark,


In more details I want to generate network of disres for all helices 
H-bonds. So I want to restraint H-bond distance between i and i+4 
atoms of the backbone.


What is the simplest way to do such task? I think that the ussage of 
genrestr -disre could be useful for such generation of the complex 
disres because of the size of my protein. But how I could define the 
restrained atoms (i, i+4 atoms ) ? In the make_ndx options I didnt 
find the most trivial sollution of the such choise. So the only 
sollution is to define each I and I+4 atoms of the backbone manualy, 
isnt it ?


Solving that will require some scripting. Because you know from genrestr 
-h that a half a matrix of distance restraints are generated for the 
index group chosen, and you only want i->i+4 restraints, you'll need a 
separate index group for every i->i+4 pair. So you can write a script 
that loops over calls to make_ndx to create a group of 2 atoms that are 
a suitable atom from i and i+4. Making make_ndx non-interactive (to call 
it from a script) is described on the website. Making a shell script to 
do that is a skill you will need to learn elsewhere.


Mark
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Re: [gmx-users] g_sas

2012-03-16 Thread afsaneh maleki

Hi,

Thanks dear Justin for useful reply,

I have a system that is contained of protein-water-ions. I want to
calculate residue SAS of protein. In the first way, I select a group
consisting protein for calculation, and then this protein for output.
At the second way, I select the whole system first for calculation,
and then protein for output. The SAS_calculations of residue protein
are different in two ways.
I have two questions.

Q1- Why results are different in two ways?
Q2-Can anyone demonstrates clearly how residue SAS of protein
calculate in two ways?
Q3- what property or quantity do I can get from The SAS_calculations
of residue protein in two ways?

Best wishes,
Afsaneh


On 3/15/12, Justin A. Lemkul  wrote:
>
>
> afsaneh maleki wrote:
>> Hello dear user,
>>
>> I have a system that is contained protein-water-ions. I used the
>> following command:
>> g_sas -f  free.xtc  -s  free.tpr   -o area  -or  res_area -oa
>> atom_area –q -nopbc
>>
>> I select the whole protein first for calculation, and then this protein
>> for output.In this way I can obtain Area per residue from "res_area" file
>> and
>> area per atom from "atom_area" file.
>>
>> How to get area per residue with data of area per atom from "atom_area"
>> file? When I average on area per atoms for a selected residue, it
>> doesn't correspond with area per residue for a selected residue from
>> "res_area".
>
> It shouldn't.  Averaging the areas per atom should not produce anything
> related
> to the constituent residue(s).  The sum of the atom areas should yield the
> residue area.  A quick look through the code seems to indicate that this is
> true, that is, the two quantities are not produced independently; residue
> area
> arises from atom area.
>
> -Justin
>
>> How to correlate area per residue for a selected residue with area per
>> atoms for a selected residue?
>>
>> Thanks in advance,
>> Afsaneh
>
> --
> 
>
> 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] Scaling/performance on Gromacs 4

2012-03-16 Thread Szilárd Páll

Hi Sara,

The bad performance you are seeing is most probably caused by the
combination of the new AMD "Interlagos" CPUs, compiler, operating
system and it is very likely the the old Gromacs version also
contributes.

In practice these new CPUs don't perform as well as expected, but that
is partly due to compilers and operating systems not having full
support for the new architecture. However, based on the quite
extensive benchmarking I've done, the with such a large system should
be considerably better than what your numbers show.

This is what you should try:
- compile Gromacs with gcc 4.6 using the "-march=bdver1" optimization flag;
- have at least 3.0 or preferably newer Linux kernel;
- if you're not required to use 4.0.x, use 4.5.

Note that you have to be careful with drawing conclusions from
benchmarking on small number of cores with large systems; you will get
artifacts from caching effects.

And now a bit of fairly technical explanation, for more details ask Google ;)

The machine you are using has AMD Interlagos CPUs based on the
Bulldozer micro-architecture. This is a new architecture, a departure
from previous AMD processors and in fact quite different from most
current CPUs. "Bulldozer cores" are not the traditional physical
cores. In fact the hardware unit is the "module" which consists of two
"half cores" (at least when it comes to floating point units). and
enable a special type of multithreading called "clustered
multithreading". This is slightly similar to the Intel cores with
Hyper-Threading.

Cheers,
--
Szilárd

On Mon, Feb 20, 2012 at 5:12 PM, Sara Campos  wrote:
> Dear GROMACS users
>
> My group has had access to a quad processor, 64 core machine (4 x Opteron
> 6274 @ 2.2 GHz with 16 cores)
> and I made some performance tests, using the following specifications:
>
> System size: 299787 atoms
> Number of MD steps: 1500
> Electrostatics treatment: PME
> Gromacs version: 4.0.4
> MPI: LAM
> Command ran: mpirun -ssi rpi tcp C mdrun_mpi ...
>
> #CPUS          Time (s)   Steps/s
> 64             195.000     7.69
> 32             192.000     7.81
> 16             275.000     5.45
> 8              381.000     3.94
> 4              751.000     2.00
> 2             1001.000     1.50
> 1             2352.000     0.64
>
> The scaling is not good. But the weirdest is the 64 processors performing
> the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC
> and I do not understand why this is happening. Can anyone help?
>
> Thanks in advance,
> Sara
>
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Re: [gmx-users] 4.6 development version

2012-03-16 Thread Szilárd Páll

The docs actually tells you:

"Native GPU acceleration is supported with the verlet cut-off scheme
(not with the group scheme) with PME, reaction-field, and plain
cut-off electrostatics."
(http://www.gromacs.org/Documentation/Parallelization_and_acceleration#GPU_acceleration)

Use the cutoff-scheme = verlet mdp option, but before you start number
crunching make sure to read the docs carefully!

Cut-off schemes: http://www.gromacs.org/Documentation/Cut-off_schemes

--
Szilárd



On Thu, Mar 15, 2012 at 10:33 AM, SebastianWaltz
 wrote:
> Dear Gromacs user,
>
> since a few days we try to get the heterogeneous parallelization on a Dell
> blade server with Tesla M2090 GPUs to work using the worksheet on the page:
>
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>
> we only get the OpenMM pure GPU version with mdrun-gpu running. Actually is
> the heterogeneous parallelization already working in the development version
> you can download using the link on the page:
>
>  http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
>
> and how can we get it running? Just adding the CMake variable GMX_GPU=ON
> when compiling mdrun did not enable the  heterogeneous parallelization.
>
> We want to use the heterogeneous parallelization used in the 4.6 version to
> find out which is the optimal GPU/CPU ratio for our studied systems, since
> we soon have to buy machines for the upgrade of our cluster.
>
> Thanks a lot
>
> yours
>
> Sebastian
>
>
>
>
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Re: [gmx-users] g_sas

2012-03-16 Thread Justin A. Lemkul




afsaneh maleki wrote:

Hi,

Thanks dear Justin for useful reply,

I have a system that is contained of protein-water-ions. I want to
calculate residue SAS of protein. In the first way, I select a group
consisting protein for calculation, and then this protein for output.
At the second way, I select the whole system first for calculation,
and then protein for output. The SAS_calculations of residue protein
are different in two ways.
I have two questions.

Q1- Why results are different in two ways?


You're asking g_sas to do two different things.  You should note that g_sas 
tells you precisely how to do the calculation (from g_sas -h):


"The calculation group should always consists of all the non-solvent atoms in 
the system. The output group can be the whole or part of the calculation group."


Choosing the whole system for the calculation group is wrong and will give an 
answer that is likely not what is needed.



Q2-Can anyone demonstrates clearly how residue SAS of protein
calculate in two ways?


Refer to the literature cited in the g_sas screen output.  Those papers will 
contain the methods.  Your second method is, however, not appropriate.  The 
first method is.



Q3- what property or quantity do I can get from The SAS_calculations
of residue protein in two ways?



Likely a meaningful one and a useless one.

-Justin

--


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] Announcement: Large biomolecule benchmark report

2012-03-16 Thread Hannes Loeffler

Thanks a a lot to you and also to Szilárd for your feedback and
encouragement.  I am very happy to see that this work is indeed useful
especially to developers.

We have no plans to make this into a 'proper' publication.  I am not
sure how much interested the simulation community would be because, to
be honest, I have no overview what has been done in this area (besides
the few benchmarks studies I have cited).

Thanks again,
Hannes.


On Thu, 15 Mar 2012 22:02:21 +0100
David van der Spoel  wrote:

> On 2012-03-15 14:37, Hannes Loeffler wrote:
> > Dear all,
> >
> > we proudly announce our third benchmarking report on (large)
> > biomolecular systems carried out on various HPC platforms.  We have
> > expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS,
> > LAMMPS and NAMD) and to five protein and protein-membrane systems
> > ranging from 20 thousand to 3 million atoms.
> >
> > Please find the report on
> > http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx
> > where we also offer the raw runtime data.  We also plan to release
> > the complete joint benchmark suite at a later date (as soon as we
> > have access to a web server with sufficient storage space).
> >
> > We are open to any questions or comments related to our reports.
> >
> It looks very interesting, and having benchmarks done by independent 
> researchers is the best way to avoid bias. The differences are quite 
> revealing, but it's also good that you point to problems compiling 
> gromacs. Is this going to be submitted for publication somewhere too?
> 
> Thanks for doing this, it must have been quite a job!
> 
> >
> > Kind regards,
> > Hannes Loeffler
> > STFC Daresbury
> 
> 

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Re: [gmx-users] Structural features for LINCS application

2012-03-16 Thread Francesco Oteri


Il 16/03/2012 01:38, Mark Abraham ha scritto:

On 16/03/2012 6:02 AM, Francesco Oteri wrote:

Dear gromacs users,
I am trying to simulate a protein (containing FeS cluster and a 
complex metal active site) using virtual site.
I've to face a problem with LINCS. In particular, if I constrain only 
h-bonds without using virtual site,
simulation runs fine but constraining "all-bonds", simulation crashes 
after a lot of LINCS warning like:


Step 356, time 0.712 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.408533, max 8.159325 (between atoms 2750 and 2754)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2750   2754   90.00.1365   1.2502  0.1365

In both cases simulation conditions are the same. The bonds causing 
problem belongs to the active site.
I am wondering if there are structural features imparing the use of 
all-bonds constraints in LINCS.
A second question is, how can I run MD with virtual site without 
all-bonds options.


Coupled constraints, such as you might have in a cluster, can be 
delicate. Equilibrating with a quite small time step can be necessary.


Mark

Hi Mark,
I've run 100ps at 0.5fs, and 1fs...but when I switch to 2fs it crashes.
I've read in the manual and it seem that triangular structures might 
introduce problem, but I dont have such a structure in my protein.
So, there are other coupled constraint that may cause problem in LINCS? 
Is it possible that the force constants can cause problem?

Or anyway, is it possible using virtual site constraining only h-bonds?

Francesco



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[gmx-users] Simulated Annealing Protocol...

2012-03-16 Thread rama david

Dear Gromacs Specialists,
I am very novice to Molecular Simulation study.
 I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..

I make my  protocol to work on simulated annealing as follow ...
(I am not writing in detail sorry for that )
1.  pdb2gmx ...
2. editconf
3. Solvent Addition
4.  Ion addition
5. Energy minimisation
6. simulated annealing
 mdp for simulated annealing is as follow...

; 7.3.3 Run Control
title   = simulated run

integrator  = md; md integrator
tinit  = 0 ; [ps] starting time for run
dt = 0.002 ; [ps] time step
for integration
nsteps  = 500   ; maximum number of
steps to integrate, 0.002 * 500 10 ns
comm_mode = Linear; remove center of mass translation
comm_grps   = Protein Non-Protein   ; group(s) for center of
mass motion removal

; 7.3.8 Output Control
nstxout = 100   ; [steps] freq to write
coordinates to trajectory
nstvout = 100   ; [steps] freq to write velocities
to trajectory
nstfout = 100   ; [steps] freq to write forces to trajectory
nstlog  = 100   ; [steps] freq to write
energies to log file
nstenergy   = 100   ; [steps] freq to write
energies to energy file
nstxtcout   = 500   ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision   = 500  ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc trajectory
energygrps  = System; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions
in all directions
rlist   = 1.0   ; [nm] cut-off distance for
the short-range neighbor list

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
rcoulomb= 1.0   ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype = cut-off   ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw= 1.4   ; [nm] distance for LJ cut-off
DispCorr= EnerPres  ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.16  ; [nm] grid spacing for FFT
grid when using PME
pme_order   = 4 ; interpolation order for PME, 4 = cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl  = berendson   ; temperature
coupling with Nose-Hoover ensemble
tc_grps = ProteinNon-Protein; groups to
couple seperately to temperature bath
tau_t   = 0.10.1; [ps] time
constant for coupling
ref_t   = 5   5   ; [K] reference
temperature for coupling
annealing   = single single
annealing_npoint= 2  2
annealing_time  = 0 20 0 20
annealing_temp  = 5 333 5 333
; 7.3.15 Pressure Coupling
pcoupl  =  parrinello-Rahman; pressure coupling
where box vectors are variable
pcoupltype  = isotropic ; pressure coupling in
x-y-z directions
tau_p   = 2.0   ; [ps] time constant
for coupling
compressibility = 4.5e-5; [bar^-1] compressibility
ref_p   = 1.0   ; [bar] reference
pressure for coupling

; 7.3.17 Velocity Generation
gen_vel = yes   ; velocity generation turned off
gen_temp= 5
; 7.3.18 Bonds
constraints  = all-bonds ; convert all bonds to constraints
constraint_algorithm= LINCS ; LINear Constraint Solver
continuation   = yes   ; apply constraints to the
start configuration
lincs_order = 4 ; highest order in the
expansion of the contraint coupling matrix
lincs_iter= 1 ; number of iterations
to correct for rotational lengthening
lincs_warnangle = 30; [degrees] maximum angle that
a bond can rotate before LINCS will complain

My Queries

1. Is My mdp file ok ???..please give me a nice protocol..
2.. Should I have to do position restrained MD before SA(simulated annealing)
(If yes then what the temp. should I have to used for NVT and NPT
(as in mdp file has lower 5 K and high 300 k  ) )
-- 
gmx-users

Re: [gmx-users] tpbconv and tpr file problem...

2012-03-16 Thread Anthony Cruz Balberdi

On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham wrote:

> On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
>
>> Hi Users:
>>
>> I was trying to calculate the energy contribution of an specific ion in
>> my simulation. After extract a given frame from the simulation, I
>> recalculate the energies of this frame with mdrun -rerun. Then I used
>> tpbconv and editconf to create a new gro file and a new tpr without the
>> ion. I tried to run mdrun -rerun with this new files but the mdrun stops
>> with the following error:
>>
>> Program mdrun, VERSION 4.5.5
>> Source code file: domdec_top.c, line: 744
>>
>> Software inconsistency error:
>> Not enough position restraint coordinates
>>
>> What could be the problem?
>>
>
> Probably some [moleculetype] now has insufficient atoms to cope with its
> position restraints, which apparently weren't edited (correctly) by the
> tpbconv subset procedure.
>
>  Any possible solution?
>>
>
> Probably depends on your use of position restraints, which would have been
> a good thing to have included in your original post


Thank for your answer and sorry for the missing information. The position
restraint is acting on the protein backbone. Since has nothing to do with
the ion, I dont understand why the error...

Anthony

>
> Mark
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Re: [gmx-users] Simulated Annealing Protocol...

2012-03-16 Thread Justin A. Lemkul




rama david wrote:

Dear Gromacs Specialists,
I am very novice to Molecular Simulation study.
 I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..

I make my  protocol to work on simulated annealing as follow ...
(I am not writing in detail sorry for that )
1.  pdb2gmx ...
2. editconf
3. Solvent Addition
4.  Ion addition
5. Energy minimisation
6. simulated annealing
 mdp for simulated annealing is as follow...

; 7.3.3 Run Control
title   = simulated run

integrator  = md; md integrator
tinit  = 0 ; [ps] starting time for run
dt = 0.002 ; [ps] time step
for integration
nsteps  = 500   ; maximum number of
steps to integrate, 0.002 * 500 10 ns
comm_mode = Linear; remove center of mass translation
comm_grps   = Protein Non-Protein   ; group(s) for center of
mass motion removal

; 7.3.8 Output Control
nstxout = 100   ; [steps] freq to write
coordinates to trajectory
nstvout = 100   ; [steps] freq to write velocities
to trajectory
nstfout = 100   ; [steps] freq to write forces to trajectory
nstlog  = 100   ; [steps] freq to write
energies to log file
nstenergy   = 100   ; [steps] freq to write
energies to energy file
nstxtcout   = 500   ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision   = 500  ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc trajectory
energygrps  = System; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions
in all directions
rlist   = 1.0   ; [nm] cut-off distance for
the short-range neighbor list

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
rcoulomb= 1.0   ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype = cut-off   ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw= 1.4   ; [nm] distance for LJ cut-off
DispCorr= EnerPres  ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.16  ; [nm] grid spacing for FFT
grid when using PME
pme_order   = 4 ; interpolation order for PME, 4 = cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl  = berendson   ; temperature
coupling with Nose-Hoover ensemble
tc_grps = ProteinNon-Protein; groups to
couple seperately to temperature bath
tau_t   = 0.10.1; [ps] time
constant for coupling
ref_t   = 5   5   ; [K] reference
temperature for coupling
annealing   = single single
annealing_npoint= 2  2
annealing_time  = 0 20 0 20
annealing_temp  = 5 333 5 333
; 7.3.15 Pressure Coupling
pcoupl  =  parrinello-Rahman; pressure coupling
where box vectors are variable
pcoupltype  = isotropic ; pressure coupling in
x-y-z directions
tau_p   = 2.0   ; [ps] time constant
for coupling
compressibility = 4.5e-5; [bar^-1] compressibility
ref_p   = 1.0   ; [bar] reference
pressure for coupling

; 7.3.17 Velocity Generation
gen_vel = yes   ; velocity generation turned off
gen_temp= 5
; 7.3.18 Bonds
constraints  = all-bonds ; convert all bonds to constraints
constraint_algorithm= LINCS ; LINear Constraint Solver
continuation   = yes   ; apply constraints to the
start configuration
lincs_order = 4 ; highest order in the
expansion of the contraint coupling matrix
lincs_iter= 1 ; number of iterations
to correct for rotational lengthening
lincs_warnangle = 30; [degrees] maximum angle that
a bond can rotate before LINCS will complain

My Queries

1. Is My mdp file ok ???..please give me a nice protocol..


It is a bad idea to generate velocities and use P-R pressure coupling at the 
same time.  Such an approach is extremely fragile and your simulation is likely 
to crash.


I assume that si

Re: [gmx-users] tpbconv and tpr file problem...

2012-03-16 Thread Mark Abraham


On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote:


On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham > wrote:


On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:

Hi Users:

I was trying to calculate the energy contribution of an
specific ion in my simulation. After extract a given frame
from the simulation, I recalculate the energies of this frame
with mdrun -rerun. Then I used tpbconv and editconf to create
a new gro file and a new tpr without the ion. I tried to run
mdrun -rerun with this new files but the mdrun stops with the
following error:

Program mdrun, VERSION 4.5.5
Source code file: domdec_top.c, line: 744

Software inconsistency error:
Not enough position restraint coordinates

What could be the problem?


Probably some [moleculetype] now has insufficient atoms to cope
with its position restraints, which apparently weren't edited
(correctly) by the tpbconv subset procedure.

Any possible solution?


Probably depends on your use of position restraints, which would
have been a good thing to have included in your original post


Thank for your answer and sorry for the missing information. The 
position restraint is acting on the protein backbone. Since has 
nothing to do with the ion, I dont understand why the error...


Anthony



OK, so maybe tpbconv subsets don't work well with position restraints. 
You can probably do what you want with a suitable combination of energy 
groups and mdrun -rerun.


Mark
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Re: [gmx-users] tpbconv and tpr file problem...

2012-03-16 Thread Anthony Cruz Balberdi

Thanks

On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham wrote:

>  On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote:
>
>
> On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham wrote:
>
>>  On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
>>
>>> Hi Users:
>>>
>>> I was trying to calculate the energy contribution of an specific ion in
>>> my simulation. After extract a given frame from the simulation, I
>>> recalculate the energies of this frame with mdrun -rerun. Then I used
>>> tpbconv and editconf to create a new gro file and a new tpr without the
>>> ion. I tried to run mdrun -rerun with this new files but the mdrun stops
>>> with the following error:
>>>
>>> Program mdrun, VERSION 4.5.5
>>> Source code file: domdec_top.c, line: 744
>>>
>>> Software inconsistency error:
>>> Not enough position restraint coordinates
>>>
>>> What could be the problem?
>>>
>>
>>  Probably some [moleculetype] now has insufficient atoms to cope with
>> its position restraints, which apparently weren't edited (correctly) by the
>> tpbconv subset procedure.
>>
>>  Any possible solution?
>>>
>>
>> Probably depends on your use of position restraints, which would have
>> been a good thing to have included in your original post
>
>
> Thank for your answer and sorry for the missing information. The position
> restraint is acting on the protein backbone. Since has nothing to do with
> the ion, I dont understand why the error...
>
> Anthony
>
>
> OK, so maybe tpbconv subsets don't work well with position restraints. You
> can probably do what you want with a suitable combination of energy groups
> and mdrun -rerun.
>
> Mark
>
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[gmx-users] Announcement: Large biomolecule benchmark report

2012-03-16 Thread chris . neale

You should absolutely publish this. it would be of great interest. You  
can mitigate your chances of running into problems with the overview  
by sending a version of the manuscript to the developers of each  
software and asking them to provide a short paragraph, each of which  
you could include in a final section of responses from the developers.


A manuscript such as this (and indeed the information that you have  
already made available) will be very useful for many reasons. One  
reason is that when new PhD students start learning about simulations,  
they tend to use the package that has been adopted by their research  
group and trust the (probably biased and partially uninformed)  
statements of their senior colleagues.


Chris.

-- original message --

Thanks a a lot to you and also to SzilÃ¡rd for your feedback and
encouragement.  I am very happy to see that this work is indeed useful
especially to developers.

We have no plans to make this into a 'proper' publication.  I am not
sure how much interested the simulation community would be because, to
be honest, I have no overview what has been done in this area (besides
the few benchmarks studies I have cited).

Thanks again,
Hannes.


On Thu, 15 Mar 2012 22:02:21 +0100
David van der Spoel  wrote:

[Hide Quoted Text]
On 2012-03-15 14:37, Hannes Loeffler wrote:
Dear all,

we proudly announce our third benchmarking report on (large)
biomolecular systems carried out on various HPC platforms.  We have
expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS,
LAMMPS and NAMD) and to five protein and protein-membrane systems
ranging from 20 thousand to 3 million atoms.

Please find the report on
http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx
where we also offer the raw runtime data.  We also plan to release
the complete joint benchmark suite at a later date (as soon as we
have access to a web server with sufficient storage space).

We are open to any questions or comments related to our reports.
It looks very interesting, and having benchmarks done by independent  
researchers is the best way to avoid bias. The differences are quite

revealing, but it's also good that you point to problems compiling
gromacs. Is this going to be submitted for publication somewhere too?

Thanks for doing this, it must have been quite a job!

Kind regards,
Hannes Loeffler
STFC Daresbury
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[gmx-users] cluster analysis of flexible peptide trajectory

2012-03-16 Thread Thomas Evangelidis

Dear GROMACS users,

Obviously RMSD-based clustering is not the best approach to find frequently
visited conformations of flexible peptides. The other approach would be to
used backbone dihedral angles to cluster the frames (i.e. with g_dih).
There are also several articles in the literature describing more
sophisticated clustering techniques used for MD trajectories of flexible
peptides (e.g. spectral clustering), yet I haven't found any program that
implements these methods to cluster the frames of a trajectory. Could
anyone please recommend me a program for cluster analysis of peptide MD
trajectories?

Thanks in advance,
Thomas
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[gmx-users] Re: Simulated Annealing Protocol

2012-03-16 Thread Dr. Vitaly V. Chaban

>  I am very novice to Molecular Simulation study.
>  I am using GROMACS 4.5.4 version .
> I completed some GROMACS tutorials , I not found any
> tutorial on Simulated Annealing..
> If Any one know the link please give me it..
>
> I make my  protocol to work on simulated annealing as follow ...
> (I am not writing in detail sorry for that )
> 1.  pdb2gmx ...
> 2. editconf
> 3. Solvent Addition
> 4.  Ion addition
> 5. Energy minimisation
> 6. simulated annealing
>  mdp for simulated annealing is as follow...
>
> ; 7.3.3 Run Control
> title                   = simulated run
>
> integrator              = md                    ; md integrator
> tinit                      = 0                     ; [ps] starting time for 
> run
> dt                         = 0.002                 ; [ps] time step
> for integration
> nsteps                  = 500               ; maximum number of
> steps to integrate, 0.002 * 500 10 ns
> comm_mode         = Linear                ; remove center of mass translation
> comm_grps           = Protein Non-Protein   ; group(s) for center of
> mass motion removal
>
> ; 7.3.8 Output Control
> nstxout                 = 100       ; [steps] freq to write
> coordinates to trajectory
> nstvout                 = 100       ; [steps] freq to write velocities
> to trajectory
> nstfout                 = 100       ; [steps] freq to write forces to 
> trajectory
> nstlog                  = 100           ; [steps] freq to write
> energies to log file
> nstenergy               = 100           ; [steps] freq to write
> energies to energy file
> nstxtcout               = 500           ; [steps] freq to write
> coordinates to xtc trajectory
> xtc_precision           = 500          ; [real] precision to write xtc
> trajectory
> xtc_grps                = System        ; group(s) to write to xtc trajectory
> energygrps              = System        ; group(s) to write to energy file
>
> ; 7.3.9 Neighbor Searching
> nstlist                 = 5             ; [steps] freq to update neighbor list
> ns_type                 = grid          ; method of updating neighbor list
> pbc                     = xyz           ; periodic boundary conditions
> in all directions
> rlist                   = 1.0           ; [nm] cut-off distance for
> the short-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
> rcoulomb                = 1.0           ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype                 = cut-off       ; twin-range cut-off with
> rlist where rvdw >= rlist
> rvdw                    = 1.4           ; [nm] distance for LJ cut-off
> DispCorr                = EnerPres      ; apply long range dispersion
> corrections for energy
>
> ; 7.3.13 Ewald
> fourierspacing          = 0.16          ; [nm] grid spacing for FFT
> grid when using PME
> pme_order               = 4             ; interpolation order for PME, 4 = 
> cubic
> ewald_rtol              = 1e-5          ; relative strength of
> Ewald-shifted potential at rcoulomb
>
> ; 7.3.14 Temperature Coupling
> tcoupl                  = berendson                   ; temperature
> coupling with Nose-Hoover ensemble
> tc_grps                 = Protein    Non-Protein        ; groups to
> couple seperately to temperature bath
> tau_t                   = 0.1        0.1                ; [ps] time
> constant for coupling
> ref_t                   = 5           5               ; [K] reference
> temperature for coupling
> annealing               = single single
> annealing_npoint        = 2  2
> annealing_time          = 0 20 0 20
> annealing_temp          = 5 333 5 333
> ; 7.3.15 Pressure Coupling
> pcoupl                  =  parrinello-Rahman    ; pressure coupling
> where box vectors are variable
> pcoupltype              = isotropic             ; pressure coupling in
> x-y-z directions
> tau_p                   = 2.0                   ; [ps] time constant
> for coupling
> compressibility         = 4.5e-5                ; [bar^-1] compressibility
> ref_p                   = 1.0                   ; [bar] reference
> pressure for coupling
>
> ; 7.3.17 Velocity Generation
> gen_vel                 = yes           ; velocity generation turned off
> gen_temp                = 5
> ; 7.3.18 Bonds
> constraints                  = all-bonds     ; convert all bonds to 
> constraints
> constraint_algorithm    = LINCS         ; LINear Constraint Solver
> continuation               = yes           ; apply constraints to the
> start configuration
> lincs_order                 = 4             ; highest order in the
> expansion of the contraint coupling matrix
> lincs_iter                    = 1             ; number of iterations
> to correct for rotational lengthening
> lincs_warnangle         = 30            ; [degrees] maximum angle that
> a bond can rotate before LINCS will complain
>
> My Queries
>
> 1. Is My mdp file ok ???..please give me a nice protocol..
> 2.. Should I have to d

[gmx-users] AZH (AZIDOHOMOALANINE) or C4 H8 N4 O2

2012-03-16 Thread SebastianWaltz

Dear Gromacs user,

I am searching for the GROMOS (best would ffG53a5) forcefield parameters
of the rather rarely used amino acid AZIDOHOMOALANINE (C4 H8 N4 O2). The
residue looks like:

http://www.chembase.com/cbid_147480.htm

Every suggestion is very welcome since it can avoid doing the
parametrization by my own saving me a lot of time.

Sincerely

Sebastian

 

 
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[gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread bestenborstel

Dear all,
I tried to install today Gromacs.
I downloaded gromacs 4.5.5, Cuda, FFTW3. 
Installation of FFTW3 and Cuda went fine so far.
I managed to execute

sudo ./configure (in the gromacs untar folder).
sudo make
sudo make install

make links did not work and I cannot find gromcas. There is no folder 
/usr/local/gromacs. I am a bit puzzled as I did install it.

I am on MacOSx 10.6.7 and I used Terminal bash during the installation process.

What can I do now to get Gromacs installed and running, please?

Thank you.
Kind regards
Gudrun 

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Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread David van der Spoel


On 2012-03-16 20:19, bestenborstel wrote:

Dear all,
I tried to install today Gromacs.
I downloaded gromacs 4.5.5, Cuda, FFTW3.
Installation of FFTW3 and Cuda went fine so far.
I managed to execute

sudo ./configure (in the gromacs untar folder).
sudo make
sudo make install


Try running again
sudo make -n install
it will not do anything, but in the terminal it will print where the 
program should be installed.



make links did not work and I cannot find gromcas. There is no folder 
/usr/local/gromacs. I am a bit puzzled as I did install it.

I am on MacOSx 10.6.7 and I used Terminal bash during the installation process.

What can I do now to get Gromacs installed and running, please?

Thank you.
Kind regards
Gudrun




--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread Justin A. Lemkul




bestenborstel wrote:

Dear all,
I tried to install today Gromacs.
I downloaded gromacs 4.5.5, Cuda, FFTW3. 
Installation of FFTW3 and Cuda went fine so far.

I managed to execute

sudo ./configure (in the gromacs untar folder).
sudo make


The above steps do not need to be executed with sudo.


sudo make install

make links did not work and I cannot find gromcas. There is no folder 
/usr/local/gromacs. I am a bit puzzled as I did install it.



When you say "make links did not work," what happened?  Was there are an error 
message of some sort?  If your installation had been successful, you would 
indeed have a /usr/local/gromacs directory.  The fact that it is not there 
suggests the installation did not actually work.  Perhaps you missed an error 
message somewhere along the way.


If I recall, /usr/local does not exist by default on Mac (I seem to remember 
having to create it myself).  Perhaps that is an issue?  If /usr/local doesn't 
exist, I don't know if Gromacs will create it or not.  Just speculation there.


-Justin


I am on MacOSx 10.6.7 and I used Terminal bash during the installation process.

What can I do now to get Gromacs installed and running, please?

Thank you.
Kind regards
Gudrun 



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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] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread bestenborstel

Thank you for your quick reply.

'make links' produces:

Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
for i in $programs; do \
   (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
make: *** [links] Error 1

I have a /usr/local/ but there is no gromacs. Not even after running again 
'sudo make -n install'
Sorry, I am not sure where to post this lengthy output.

Thank you for your help.
Kind regards
Gudrun 

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Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread David van der Spoel


On 2012-03-16 20:49, bestenborstel wrote:

Thank you for your quick reply.

'make links' produces:

Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin&&  programs=`ls`&&  cd /usr/local/bin&&  \
for i in $programs; do \
   (test ! -f $i&&  ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
make: *** [links] Error 1

I have a /usr/local/ but there is no gromacs. Not even after running again 
'sudo make -n install'
Sorry, I am not sure where to post this lengthy output.


-n means "not really"
run it without to install.
But do you have permission to write in /usr/local?


Thank you for your help.
Kind regards
Gudrun




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread bestenborstel

Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do 
whatever I can :-)
What do you ask me please to do?

Am 16.03.2012 um 19:54 schrieb David van der Spoel:

> On 2012-03-16 20:49, bestenborstel wrote:
>> Thank you for your quick reply.
>> 
>> 'make links' produces:
>> 
>> Saturn:gromacs-4.5.5 gudrun$ make links
>> cd /usr/local/gromacs/bin&&  programs=`ls`&&  cd /usr/local/bin&&  \
>>  for i in $programs; do \
>> (test ! -f $i&&  ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
>>  done
>> /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
>> make: *** [links] Error 1
>> 
>> I have a /usr/local/ but there is no gromacs. Not even after running again 
>> 'sudo make -n install'
>> Sorry, I am not sure where to post this lengthy output.
>> 
> -n means "not really"
> run it without to install.
> But do you have permission to write in /usr/local?
> 
>> Thank you for your help.
>> Kind regards
>> Gudrun
>> 
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread David van der Spoel


On 2012-03-16 21:03, bestenborstel wrote:

Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do 
whatever I can :-)
What do you ask me please to do?

sudo make install
and check on the screen where the stuff is copied to.



Am 16.03.2012 um 19:54 schrieb David van der Spoel:


On 2012-03-16 20:49, bestenborstel wrote:

Thank you for your quick reply.

'make links' produces:

Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin&&   programs=`ls`&&   cd /usr/local/bin&&   \
for i in $programs; do \
   (test ! -f $i&&   ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
make: *** [links] Error 1

I have a /usr/local/ but there is no gromacs. Not even after running again 
'sudo make -n install'
Sorry, I am not sure where to post this lengthy output.


-n means "not really"
run it without to install.
But do you have permission to write in /usr/local?


Thank you for your help.
Kind regards
Gudrun




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell&  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread bestenborstel

Did run sudo make install again, but before I executed configure with 
prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before 
manually. Content in the gromacs folder: bin   include lib share

Gromacs finished again with:

GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.

Please run "make tests" now to verify your installation.

If you want links to the executables in /usr/local/bin,
you can issue "make links" now.

Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also 
don't really know how to update my PATH variable. 
Do I have to execute 'make test' as the Gromacs page says test set is broken?
Finally, is there something like 'make clean'  to allow for a proper, clean 
re-installation?

I thought I better ask again.
Sorry.
Gudrun

Am 16.03.2012 um 20:05 schrieb David van der Spoel:

> On 2012-03-16 21:03, bestenborstel wrote:
>> Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do 
>> whatever I can :-)
>> What do you ask me please to do?
> sudo make install
> and check on the screen where the stuff is copied to.
> 
>> 
>> Am 16.03.2012 um 19:54 schrieb David van der Spoel:
>> 
>>> On 2012-03-16 20:49, bestenborstel wrote:
 Thank you for your quick reply.

 'make links' produces:

 Saturn:gromacs-4.5.5 gudrun$ make links
 cd /usr/local/gromacs/bin&&   programs=`ls`&&   cd /usr/local/bin&&   \
for i in $programs; do \
   (test ! -f $i&&   ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
 /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
 make: *** [links] Error 1

 I have a /usr/local/ but there is no gromacs. Not even after running again 
 'sudo make -n install'
 Sorry, I am not sure where to post this lengthy output.

>>> -n means "not really"
>>> run it without to install.
>>> But do you have permission to write in /usr/local?
>>> 
 Thank you for your help.
 Kind regards
 Gudrun

>>> 
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell&  Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www interface 
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread Justin A. Lemkul




bestenborstel wrote:

Did run sudo make install again, but before I executed configure with 
prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before 
manually. Content in the gromacs folder: bin   include lib share

Gromacs finished again with:

GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.

Please run "make tests" now to verify your installation.

If you want links to the executables in /usr/local/bin,
you can issue "make links" now.


Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. 


You need sudo.  It will write links into /usr/local/bin.  It is not strictly 
necessary, as you can follow:


http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation

The GMXRC script magically configures your environment for you.


Do I have to execute 'make test' as the Gromacs page says test set is broken?


No, it won't do anything.


Finally, is there something like 'make clean'  to allow for a proper, clean 
re-installation?



Yes.

-Justin


I thought I better ask again.
Sorry.
Gudrun


Am 16.03.2012 um 20:05 schrieb David van der Spoel:


On 2012-03-16 21:03, bestenborstel wrote:

Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do 
whatever I can :-)
What do you ask me please to do?

sudo make install
and check on the screen where the stuff is copied to.


Am 16.03.2012 um 19:54 schrieb David van der Spoel:


On 2012-03-16 20:49, bestenborstel wrote:

Thank you for your quick reply.

'make links' produces:

Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin&&   programs=`ls`&&   cd /usr/local/bin&&   \
for i in $programs; do \
   (test ! -f $i&&   ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
make: *** [links] Error 1

I have a /usr/local/ but there is no gromacs. Not even after running again 
'sudo make -n install'
Sorry, I am not sure where to post this lengthy output.


-n means "not really"
run it without to install.
But do you have permission to write in /usr/local?


Thank you for your help.
Kind regards
Gudrun



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell&  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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send it to gmx-users-requ...@gromacs.org.
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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] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread bestenborstel

Again 'sudo make links'  gives:

cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
for i in $programs; do \
   (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done

Is this good or bad, please?

g_luck is located for example now in /usr/local/bin/g_luck when I do 'which 
g_luck'
Would you recommend to re-install, although it seems to work now? 
Thank you for your help.

Thank you.
Kind regards
Gudrun


Am 16.03.2012 um 20:28 schrieb Justin A. Lemkul:

> 
> 
> bestenborstel wrote:
>> Did run sudo make install again, but before I executed configure with 
>> prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before 
>> manually. Content in the gromacs folder: bininclude lib share
>> Gromacs finished again with:
>> GROMACS is installed under /usr/local/gromacs.
>> Make sure to update your PATH and MANPATH to find the
>> programs and unix manual pages, and possibly LD_LIBRARY_PATH
>> or /etc/ld.so.conf if you are using dynamic libraries.
>> Please run "make tests" now to verify your installation.
>> If you want links to the executables in /usr/local/bin,
>> you can issue "make links" now.
>> Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also 
>> don't really know how to update my PATH variable. 
> 
> You need sudo.  It will write links into /usr/local/bin.  It is not strictly 
> necessary, as you can follow:
> 
> http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation
> 
> The GMXRC script magically configures your environment for you.
> 
>> Do I have to execute 'make test' as the Gromacs page says test set is broken?
> 
> No, it won't do anything.
> 
>> Finally, is there something like 'make clean'  to allow for a proper, clean 
>> re-installation?
> 
> Yes.
> 
> -Justin
> 
>> I thought I better ask again.
>> Sorry.
>> Gudrun
>> Am 16.03.2012 um 20:05 schrieb David van der Spoel:
>>> On 2012-03-16 21:03, bestenborstel wrote:
 Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can 
 do whatever I can :-)
 What do you ask me please to do?
>>> sudo make install
>>> and check on the screen where the stuff is copied to.
>>> 
 Am 16.03.2012 um 19:54 schrieb David van der Spoel:
 
> On 2012-03-16 20:49, bestenborstel wrote:
>> Thank you for your quick reply.
>> 
>> 'make links' produces:
>> 
>> Saturn:gromacs-4.5.5 gudrun$ make links
>> cd /usr/local/gromacs/bin&&   programs=`ls`&&   cd /usr/local/bin&&   \
>>  for i in $programs; do \
>> (test ! -f $i&&   ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
>>  done
>> /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
>> make: *** [links] Error 1
>> 
>> I have a /usr/local/ but there is no gromacs. Not even after running 
>> again 'sudo make -n install'
>> Sorry, I am not sure where to post this lengthy output.
>> 
> -n means "not really"
> run it without to install.
> But do you have permission to write in /usr/local?
> 
>> Thank you for your help.
>> Kind regards
>> Gudrun
>> 
> 
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell&  Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> -- 
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>> -- 
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www interface 
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
> 
> 
> 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
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive

Re: [gmx-users] Gromacs installation question: Where is my Gromacs?

2012-03-16 Thread Justin A. Lemkul




bestenborstel wrote:

Again 'sudo make links'  gives:

cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
for i in $programs; do \
   (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done

Is this good or bad, please?



In the absence of an error message, nothing is wrong.


g_luck is located for example now in /usr/local/bin/g_luck when I do 'which 
g_luck'
Would you recommend to re-install, although it seems to work now? 


I see no need for a reinstall.  It appears to be working as expected.

-Justin


Thank you for your help.

Thank you.
Kind regards
Gudrun


Am 16.03.2012 um 20:28 schrieb Justin A. Lemkul:



bestenborstel wrote:

Did run sudo make install again, but before I executed configure with 
prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before 
manually. Content in the gromacs folder: bin   include lib share
Gromacs finished again with:
GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.
Please run "make tests" now to verify your installation.
If you want links to the executables in /usr/local/bin,
you can issue "make links" now.
Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. 

You need sudo.  It will write links into /usr/local/bin.  It is not strictly 
necessary, as you can follow:

http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation

The GMXRC script magically configures your environment for you.


Do I have to execute 'make test' as the Gromacs page says test set is broken?

No, it won't do anything.


Finally, is there something like 'make clean'  to allow for a proper, clean 
re-installation?

Yes.

-Justin


I thought I better ask again.
Sorry.
Gudrun
Am 16.03.2012 um 20:05 schrieb David van der Spoel:

On 2012-03-16 21:03, bestenborstel wrote:

Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do 
whatever I can :-)
What do you ask me please to do?

sudo make install
and check on the screen where the stuff is copied to.


Am 16.03.2012 um 19:54 schrieb David van der Spoel:


On 2012-03-16 20:49, bestenborstel wrote:

Thank you for your quick reply.

'make links' produces:

Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin&&   programs=`ls`&&   cd /usr/local/bin&&   \
for i in $programs; do \
   (test ! -f $i&&   ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
make: *** [links] Error 1

I have a /usr/local/ but there is no gromacs. Not even after running again 
'sudo make -n install'
Sorry, I am not sure where to post this lengthy output.


-n means "not really"
run it without to install.
But do you have permission to write in /usr/local?


Thank you for your help.
Kind regards
Gudrun


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell&  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--


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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[gmx-users] g_sas; could not find a Van der Waals radius

2012-03-16 Thread afsaneh maleki

Hi,
I have a system that is contained of Protein-DOPC-SOL-Ions. I want to
calculate residue SAS of protein.The calculation group consists of all
the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14
ion),and then protein for output. Force files used for protein and
DOPC are ffg53a6 and Berger respectively.

When I use g_sas I obtain the following message:
WARNING: could not find a Van der Waals radius for 125 atoms.

I have two questions.
Q1- This warning is important?
Q2-Is the valid source to get data for Van der Waals radius of
phosphorous atom to insert in the vdwradii.dat file? I think this
warning is about phosphorous atoms of DOPC. what is  Van der Waals
radius of phosphorous atoms that will be right for this goal?

Thanks very much in advance,
afsaneh
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[gmx-users] pdb2gmx error message

2012-03-16 Thread Wholly Peach

Dear All,
 
I meet the following error message for pdb2gmx. Please let me know how to solve 
this problem.
 
Cheers,
 
Wholly  Program pdb2gmx, VERSION 3.3.3
Source code file: futil.c, line: 542
Fatal error:
Library file FF.dat not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)-- 
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[gmx-users] genion -pname no NA molecule (sodium) type

2012-03-16 Thread Wholly Peach

 Dear All,
I use the following to neutralize the charge
"genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 
8",
Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top 
-o em.tpr"".
However the feedback says there is no Na (sodium) moleculetype.
I am looking forward to getting a reply from you on it, which is a fatal 
problem.
Cheers,
Wholly-- 
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Re: [gmx-users] genion -pname no NA molecule (sodium) type

2012-03-16 Thread Mark Abraham


On 17/03/2012 4:48 PM, Wholly Peach wrote:

Dear All,
  
I use the following to neutralize the charge
  
"genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8",
  
Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr"".
  
However the feedback says there is no Na (sodium) moleculetype.




Your force field defines [moleculetype] sections for ions in its 
ions.itp file. Go and look at it, compare with your .top and see what 
the problem is. Atom names, residue names and moleculetype names are all 
different things, and each part of your .top must match the right name 
at the right time.


Mark
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Re: [gmx-users] genion -pname no NA molecule (sodium) type

2012-03-16 Thread Wholly Peach

Will you please tell me where can I find the ions.itp file?
 
I am looking forward to getting your reply.
 
Wholly
 


 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Saturday, 17 March 2012 3:55 PM
Subject: Re: [gmx-users] genion -pname no NA molecule (sodium) type
  

On 17/03/2012 4:48 PM, Wholly Peach wrote: 

>Dear All,  
>I use the following to neutralize the charge  
>"genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 
>8",  
>Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p 
>topol.top -o em.tpr"".  
>However the feedback says there is no Na (sodium) moleculetype. 
>  
Your force field defines [moleculetype] sections for ions in its
  ions.itp file. Go and look at it, compare with your .top and see
  what the problem is. Atom names, residue names and moleculetype
  names are all different things, and each part of your .top must
  match the right name at the right time.

Mark
  
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Re: [gmx-users] genion -pname no NA molecule (sodium) type

2012-03-16 Thread Mark Abraham


On 17/03/2012 4:57 PM, Wholly Peach wrote:

Will you please tell me where can I find the ions.itp file?



http://www.gromacs.org/Documentation/Terminology/Environment_Variables

Mark
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[gmx-users] g_sas; could not find a Van der Waals radius

[gmx-users] pdb2gmx error message

[gmx-users] genion -pname no NA molecule (sodium) type

Re: [gmx-users] genion -pname no NA molecule (sodium) type

Re: [gmx-users] genion -pname no NA molecule (sodium) type

Re: [gmx-users] genion -pname no NA molecule (sodium) type

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