date:20111031

Hello Ahmet:

The warnings originating from the LINCS algorithm are dee to either
incorrect topology (TOP file) of certain particle or bad initial
configuration (GRO file).

If you don't provide this information about your problematic system,
there is no chance to help you.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA



2011/10/29 ahmet yıldırım :
> Dear Dr. Chaban,
>
> I am studying on protein modelling using Gromacs software for 1-2 years. I
> have lincs warning error. I obtained the error "lincs warning" after "mdrun
> -deffnm protein-RUN" (finally step). I could not figure out this problem for
> weeks :-(((
>
> If can you help me I will be very very happy? :-(
>
> Sincerely yours
>
> Department of Physics, Siirt University, Siirt, Turkey
>
> --
> Dr.Ahmet YILDIRIM
>
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[gmx-users] Prosessing of the pre-eqilibrated lipid bilayer

Dear Gromacs Users!

I wounder to know about possible algorithm of preparation of the existing
lipid bilayer for further simulation.
E.g I have some pre-equilibrated bilayer consisted of symmetrical lipid
organization. Now I'd like to remove some lipids from the edges of my
bilayer to reduce overall ammounts lipids but dont perturb symmetry of the
system. Then I'd like to place this bilayer to the rombic box (
corresponded to the organzation of the new bilayer system).
How I could to realise such operation of the lipid removing ?

In addition I'd like to check Area per lipid value during that removing.
How this could be done?

James
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[gmx-users] how to calculate the force between two groups

2011-10-31 Thread Tom

Dear Gromacs Users,

I have a question about how to ouput the force between two groups.

Suppose the system consists of the groups: A, B, C and D.
I need the force only between the groups A and B.

g_traj looks only to be able to report the overal forces and cann not distiguish
the forces from different groups.

Is there any cunning way to do it.

Thanks,

Tom
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Re: [gmx-users] problem with Threading during run

2011-10-31 Thread lina

On Mon, Oct 31, 2011 at 9:28 AM, Sanku M  wrote:
> Hi,
>  I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to
> make use of threading introduced in gromacs 4.5.x series, it does not work.
>  After issuing command like mdrun -v -s , I expected that for my 8-core
> processor which is not running any other jobs, the threading will show one
> job with 800 % cpu usage. But, it is showing 100 % cpu usage hence using
> only 1 of the 8 processors. I was wondering whether there is any command

mdrun -t number_of_processors

> line I need to use to ensure the gromacs understands that there is 8
> processors in a core and force make full use of the entire machine.
> I have tried the same thing in another different cluster where I found that
> threading works with showing 800 % cpu usage . But, for this cluster , the
> threading does not work.
and make sure during your compile process, enable --threads

> Any help will be appreciated.
> Sanku
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Re: [gmx-users] how to calculate the force between two groups


On 31/10/2011 4:05 AM, Tom wrote:

Dear Gromacs Users,

I have a question about how to ouput the force between two groups.

Suppose the system consists of the groups: A, B, C and D.
I need the force only between the groups A and B.

g_traj looks only to be able to report the overal forces and cann not distiguish
the forces from different groups.

Is there any cunning way to do it.

mdrun -rerun  with well-chosen energy group exclusions probably works 
for you.


Mark
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[gmx-users] average structure

2011-10-31 Thread larifsofiene


Greeting
i'm doing a MD simulation for a monomeric protein over 10 ns, my 
question is :


* for my MD how do i know that it has equilibrated and suitable for 
study ?,is it RMSD , Radius of gyration and potential energy stability 
enough ? OR should i look for other parameters and do multiple 
simulation with the same results ?


* for simulation structure study should i use an average structure 
(g_covar or grmsf) OR should i use the last trajectory from the 
simulation (the 10 th ns trajectory )


*if i use average structure should i delete hydrogen before looking for 
hydrogen bonds ?,because average structure with it's original H give 
abnormal H bonds.


Thanks very much :)
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[gmx-users] position restraints on heavy atoms or all?

2011-10-31 Thread Yun Shi

Hello all,

I am using amber99SB to model an antibody with organic ligands.

I know we could choose to restrain all atoms or only heavy atoms during the
equilibration. But I wonder if this really matters for my system. As far as
I know, equilibration is aimed at getting the temperature and pressure
right, mainly for the solvent. And as long as we are going to do a 'real' MD
production run without restraints, it should not matter too much how we
restrained the antibody and ligands?

I am not if I am right about this. Any suggestions?

Thanks,
Yun
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Re: [gmx-users] Normal Mode Analysis

Mark, hello!

I think that there is some error durins saving of my minimization data

As the result of the minimization I've obtained

(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy  =  2.08789280994511e+03
Maximum force =  3.01715687185776e-04 on atom 58
Norm of force =  3.0930131065e-05

So the Fmax is sufficient low

But when I've load this data for NMA I've obtained

(2)
Maximum force: 8.41270e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.


So the Fmax is indeed very big for NMA but why it's not the same as in the
(1)?

This is my script for NMA wich indicate that I've load to NMA suitable data

# Steep
grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr

mdrun_d -v -deffnm minimizedS


# Grad
grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o
minimizedGRAD.tpr

mdrun_d -v -deffnm minimizedGRAD


# NMA
grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr

mdrun_d -v -deffnm fornma -mtx nm.mtx




Where is the error?


James


2011/10/28 Mark Abraham 

>  On 28/10/2011 2:30 AM, James Starlight wrote:
>
> That's energy ouptut from minimization with that parametries ( there is
> also 1 step of steep minimization before that )
>
> integrator= l-bfgs
> emtol= 0.001
> emstep  = 0.001  ; Energy step size
> nsteps= 50  ; Maximum number of (minimization)
> steps to perform
>
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist= 1; Frequency to update the neighbor list and long
> range forces
> ns_type= grid; Method to determine neighbor list (simple,
> grid)
> rlist= 1.2; Cut-off for making neighbor list (short range
> forces)
> coulombtype= Shift
> rcoulomb= 1.0
> rcoulomb_switch= 0.7
> vdwtype = Shift
> rvdw= 1.0
> rvdw_switch = 0.7
>
>
> Output:
>
> Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 3646 steps
> Potential Energy  =  2.28946300988746e+03
> Maximum force =  8.47298141911052e-04 on atom 100
> Norm of force =  3.90346504086500e-04
>
> I'm not sure about the succses of that minimization due to the big Epot.
>
>
>
>
>  You look like you are shuffling deck chairs on the Titanic. I suggested
> you actually go and visualize your input and output trajectories. Sadly
> that doesn't seem to have happened.
>
> Mark
>
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Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

2011-10-31 Thread Mirco Wahab


On 24.10.2011 23:23, Szilárd Páll wrote:

I've just realized that both you and the similar report you linked to
were using CMake 2.8.3. If you don't succeed could you try another
CMake version?


I could replicate the error with the simple cmake inviocation you proposed in 
your reply:


cmake ../gromacs-4.5.5 -DGMX_MPI=ON  -DCMAKE_INSTALL_PREFIX=/tmp/gromacs-4.5 &&
make mdrun -j4 &&  make install-mdrun


This fails w/cmake 2.8.3 as before.

Then, I installed cmake 2.8.6 on the same system, cleaned the
build path and rerunned the build.

Your suspicion was correct, *it now works* (w/2.8.6).

So, 2.8.3 messes up the build process independend
of the specific tool chain, maybe this could be
added as a warning to the compilation instructions.

BTW, I even managed to get an win64 (multithreaded,
non-MPI) executeable displaying respectable performance
by using  windows-cmake, visual studio 2010 SP1,
visual studio sdk SP1 7.1/64, and Nasm-win.

Thank you very much for your help.

M.
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Re: [gmx-users] System heating up during MD run? (Implicit solvent)

2011-10-31 Thread Per Larsson

Hi

There has been a number of reports lately about ill-behaving simulations using 
implicit solvent. I'm currently trying to investigate the cause of this, as 
such simulations used to work very nice in our hands.

In the meantime I would advice to use implicit solvent with caution.

Thanks
/Per

Skickat från min iPhone

30 okt 2011 kl. 02:10 skrev Matt Larson :

> I've been having problems getting implicit solvent systems (which are
> probably fairly experiment still in gromacs) to work correctly.  I've
> been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
> simulation.  By the end of the simulation, the temperature has risen
> from 300 K to 496 K - and the protein unfolds.  It was supposed to
> maintain temp at 300 K.
> 
> I have an a non-zero total charge of -6.99.  With explicit
> solvent, I would normally add the appropriate matching ions, but with
> implicit solvent what should you do?   Could the non-zero total charge
> result in heating?  Or is the thermostat not working well enough
> (should I change tau-t or ref-t?)
> 
> Here is my md.mdp file:
> 
> 
> constraints =  all-bonds ; trying..
> integrator  =  md
> dt  =  0.002; ps !
> nsteps  =  100
> nstlist =  10
> ns_type =  grid
> rlist   =  1.0
> coulombtype =  cut-off
> fourierspacing  =  0.16
> vdwtype =  cut-off
> rcoulomb=  1.0
> rvdw=  1.0  ; important for neighbor searching
> pbc =  no   ; no periodic boundary conditions
> epsilon_rf  =  0
> rgbradii=  1.0  ; must equal rlist, rcoulomb, rvdw
> comm_mode   =  angular
> optimize_fft= yes
> 
> implicit_solvent= GBSA
> gb_algorithm= OBC
> gb_epsilon_solvent  = 80
> sa_surface_tension  = 2.25936
> 
> nstcomm = 10
> nstxout = 1000
> nstxtcout   = 1000
> nstvout = 0
> nstfout = 0
> 
> tcoupl  = andersen
> tc-grps = system
> tau-t   = 0.1
> ref-t   = 300
> 
> gen_vel = yes
> gen_temp= 300
> gen_seed= -1
> 
> -
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[gmx-users] Structure preparation for the simulation

Dear Gromacs Users!


I'd like to know about external software wich could be used for structure
processing for the futher simulation in Gromacs. Today I've tried one of the
most popular such software Amber tools but I've forced with problems during
compilation of it ") So I'm looking for possible analogues )

First of all I'm intresting in software for the addition different CAPing
groups to N and C termi of my protein.

Is there any plugins for Pymol or VMD for such purposes? I've loked for this
option in both of that software but couldnot  find


Thank you for your help,

James
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Re: [gmx-users] Normal Mode Analysis




James Starlight wrote:

Mark, hello!

I think that there is some error durins saving of my minimization data

As the result of the minimization I've obtained

(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy  =  2.08789280994511e+03
Maximum force =  3.01715687185776e-04 on atom 58
Norm of force =  3.0930131065e-05

So the Fmax is sufficient low

But when I've load this data for NMA I've obtained

(2)
Maximum force: 8.41270e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.


So the Fmax is indeed very big for NMA but why it's not the same as in 
the (1)?


This is my script for NMA wich indicate that I've load to NMA suitable data

# Steep
grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr

mdrun_d -v -deffnm minimizedS


# Grad
grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o 
minimizedGRAD.tpr


mdrun_d -v -deffnm minimizedGRAD


# NMA
grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr

mdrun_d -v -deffnm fornma -mtx nm.mtx




Where is the error?




You're using the unminimized coordinates as input into NMA.  The file 
"minimizedGRAD.tpr" contains the configuration before doing L-BFGS minimization, 
so it is not sufficiently minimized.


http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

-Justin

--


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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] System heating up during MD run? (Implicit solvent)



I would also add that the settings provided below probably produce severe cutoff 
artifacts.  In my experience, the only stable settings are those of the 
all-vs-all kernel (with infinite cutoffs).


-Justin

Per Larsson wrote:

Hi

There has been a number of reports lately about ill-behaving simulations using 
implicit solvent. I'm currently trying to investigate the cause of this, as 
such simulations used to work very nice in our hands.

In the meantime I would advice to use implicit solvent with caution.

Thanks
/Per

Skickat från min iPhone

30 okt 2011 kl. 02:10 skrev Matt Larson :


I've been having problems getting implicit solvent systems (which are
probably fairly experiment still in gromacs) to work correctly.  I've
been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
simulation.  By the end of the simulation, the temperature has risen
from 300 K to 496 K - and the protein unfolds.  It was supposed to
maintain temp at 300 K.

I have an a non-zero total charge of -6.99.  With explicit
solvent, I would normally add the appropriate matching ions, but with
implicit solvent what should you do?   Could the non-zero total charge
result in heating?  Or is the thermostat not working well enough
(should I change tau-t or ref-t?)

Here is my md.mdp file:


constraints =  all-bonds ; trying..
integrator  =  md
dt  =  0.002; ps !
nsteps  =  100
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype =  cut-off
fourierspacing  =  0.16
vdwtype =  cut-off
rcoulomb=  1.0
rvdw=  1.0  ; important for neighbor searching
pbc =  no   ; no periodic boundary conditions
epsilon_rf  =  0
rgbradii=  1.0  ; must equal rlist, rcoulomb, rvdw
comm_mode   =  angular
optimize_fft= yes

implicit_solvent= GBSA
gb_algorithm= OBC
gb_epsilon_solvent  = 80
sa_surface_tension  = 2.25936

nstcomm = 10
nstxout = 1000
nstxtcout   = 1000
nstvout = 0
nstfout = 0

tcoupl  = andersen
tc-grps = system
tau-t   = 0.1
ref-t   = 300

gen_vel = yes
gen_temp= 300
gen_seed= -1

-
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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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[gmx-users] Nonbonded energy Protein-Ligands

2011-10-31 Thread Steven Neumann

Dear Gmx Users,

My system consists of 10 ligands and protein. I am calculating the hydrogen
bonds between each residue and my ligands (LIG). The overall charge of each
ligand is zero.
I used:

g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num
RESIDUEwithLigandsHbond.xvg

And I found one residue with avergae number of hydrogen bonds = 2.2 per
time frame which is quite a lot comparing to other residues.

Then I calculated the nonbonded energy between this residue and my 10
ligands:

g_energy -f md2.edr -s topol.tpr -o 127LJwithLIG.xvg - SR - LJ energy
res127-LIG = 0.659 kcal/mol


g_energy -f md2.edr -s topol.tpr -o 127CoulombWithLIG.xvg -SR - Coulomb
res127-LIG = -32.579 kcal/mol



The total energy (nonbonded) as a sum of LJ and Coulomb = -31.919 kcal/mol



My question is: how is it possible that contribution of Coulombic
attraction is so high if the overall charge of each ligand is zero? And why
the LJ potential seems to be slightly repulisve? Is the evidence of
hydrophobic attraction?



Thank you in advance,



Steven
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Re: [gmx-users] average structure


On 31/10/2011 7:39 PM, larifsofiene wrote:

Greeting
i'm doing a MD simulation for a monomeric protein over 10 ns, my 
question is :


* for my MD how do i know that it has equilibrated and suitable for 
study ?,is it RMSD , Radius of gyration and potential energy stability 
enough ? OR should i look for other parameters and do multiple 
simulation with the same results ?


If those and any observables related to your point of interest look 
converged over time (compare averages from different parts of the 
trajectory) then things are probably fine. It depends how ordered your 
protein should be...


* for simulation structure study should i use an average structure 
(g_covar or grmsf) OR should i use the last trajectory from the 
simulation (the 10 th ns trajectory )


*if i use average structure should i delete hydrogen before looking 
for hydrogen bonds ?,because average structure with it's original H 
give abnormal H bonds.


See the http://www.gromacs.org/Documentation/FAQs about average structures.

Mark
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Re: [gmx-users] Nonbonded energy Protein-Ligands


On 31/10/2011 10:19 PM, Steven Neumann wrote:

Dear Gmx Users,
My system consists of 10 ligands and protein. I am calculating the 
hydrogen bonds between each residue and my ligands (LIG). The overall 
charge of each ligand is zero.

I used:
g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 
RESIDUEwithLigandsHbond.xvg
And I found one residue with avergae number of hydrogen bonds = 2.2 
per time frame which is quite a lot comparing to other residues.
Then I calculated the nonbonded energy between this residue and my 10 
ligands:
g_energy -f md2.edr -s topol.tpr -o 127LJwithLIG.xvg - SR - LJ 
energy res127-LIG = 0.659 kcal/mol


g_energy -f md2.edr -s topol.tpr -o 127CoulombWithLIG.xvg -SR - 
Coulomb res127-LIG = -32.579 kcal/mol


The total energy (nonbonded) as a sum of LJ and Coulomb = -31.919 kcal/mol

My question is: how is it possible that contribution of Coulombic 
attraction is so high if the overall charge of each ligand is zero?




Consider two neutral dipoles fixed either parallel or anti-parallel to 
each other.


And why the LJ potential seems to be slightly repulisve? Is the 
evidence of hydrophobic attraction?




First, define "hydrophobic attraction" :-)

Mark
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Re: [gmx-users] problem with Threading during run


On 31/10/2011 3:36 PM, lina wrote:

On Mon, Oct 31, 2011 at 9:28 AM, Sanku M  wrote:

Hi,
  I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to
make use of threading introduced in gromacs 4.5.x series, it does not work.
  After issuing command like mdrun -v -s , I expected that for my 8-core
processor which is not running any other jobs, the threading will show one
job with 800 % cpu usage. But, it is showing 100 % cpu usage hence using
only 1 of the 8 processors. I was wondering whether there is any command

mdrun -t number_of_processors


No, mdrun -nt will specify a number of processors, but I have never 
heard of any system where the default (0 meaning to guess) does not lead 
to a correct result.



line I need to use to ensure the gromacs understands that there is 8
processors in a core and force make full use of the entire machine.
I have tried the same thing in another different cluster where I found that
threading works with showing 800 % cpu usage . But, for this cluster , the
threading does not work.

and make sure during your compile process, enable --threads


configure --enable-threads works, but this is enabled by default.

Mark




Any help will be appreciated.
Sanku
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[gmx-users] Number of nodes

2011-10-31 Thread Kavyashree M

Dear Users,

I was trying to run a simulation (gromacs4.5.3)
on a Bluegene/L machine. But I was unable to run.
System admin say that I need to change the input
file. I am not sure what needs to be changed in the
input file which specifies no. of nodes usage.

I am not familiar with the bluegene machines. Kindly
suggest the possible solutions.

Thanking you
With Regards
Kavya
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[gmx-users] Re: Dear Chaban lincs warning

ahmet yıldırım:

If you want a personal mentoria, you will need to pay for it first. If
you strive to get a FREE help, all correspondence should be kept in
the mailing list to save up an archive for other gromacs users.

Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA



2011/10/31 ahmet yıldırım :
> Please, dont send any reply. I dont want your helps. You send to gmx user
> list my mail without permission from me :(:(:(. Please dont send me any
> mail/reply
>
>
>
> 31 Ekim 2011 09:27 tarihinde ahmet yıldırım  yazdı:
>>
>> Dear Dr. Chaban,
>>
>> Firstly, thanks for your reply. I send you the input files that I used.
>> Please look at attached files. By the way, I am using Gromacs 4.5.3
>>
>> Regards
>>
>>
>>
>> 30 Ekim 2011 02:53 tarihinde Dr. Vitaly V. Chaban 
>> yazdı:
>>>
>>> Hello Ahmet:
>>>
>>> The warnings originating from the LINCS algorithm are dee to either
>>> incorrect topology (TOP file) of certain particle or bad initial
>>> configuration (GRO file).
>>>
>>> If you don't provide this information about your problematic system,
>>> there is no chance to help you.
>>>
>>> --
>>> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
>>> Univ. Rochester, Rochester, New York 14627-0216
>>> THE UNITED STATES OF AMERICA
>>>
>>>
>>>
>>> 2011/10/29 ahmet yıldırım :
>>> > Dear Dr. Chaban,
>>> >
>>> > I am studying on protein modelling using Gromacs software for 1-2
>>> > years. I
>>> > have lincs warning error. I obtained the error "lincs warning" after
>>> > "mdrun
>>> > -deffnm protein-RUN" (finally step). I could not figure out this
>>> > problem for
>>> > weeks :-(((
>>> >
>>> > If can you help me I will be very very happy? :-(
>>> >
>>> > Sincerely yours
>>> >
>>> > Department of Physics, Siirt University, Siirt, Turkey
>>> >
>>> > --
>>> > Dr.Ahmet YILDIRIM
>>> >
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>
>
>
> --
> Ahmet YILDIRIM
>
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[gmx-users] Re: Dear Chaban lincs warning

You should provide topology file, I do NOT need your MDP files.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA



2011/10/31 ahmet yıldırım :
> Dear Dr. Chaban,
>
> Firstly, thanks for your reply. I send you the input files that I used.
> Please look at attached files. By the way, I am using Gromacs 4.5.3
>
> Regards
>
>
>
> 30 Ekim 2011 02:53 tarihinde Dr. Vitaly V. Chaban 
> yazdı:
>>
>> Hello Ahmet:
>>
>> The warnings originating from the LINCS algorithm are dee to either
>> incorrect topology (TOP file) of certain particle or bad initial
>> configuration (GRO file).
>>
>> If you don't provide this information about your problematic system,
>> there is no chance to help you.
>>
>> --
>> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
>> Univ. Rochester, Rochester, New York 14627-0216
>> THE UNITED STATES OF AMERICA
>>
>>
>>
>> 2011/10/29 ahmet yıldırım :
>> > Dear Dr. Chaban,
>> >
>> > I am studying on protein modelling using Gromacs software for 1-2 years.
>> > I
>> > have lincs warning error. I obtained the error "lincs warning" after
>> > "mdrun
>> > -deffnm protein-RUN" (finally step). I could not figure out this problem
>> > for
>> > weeks :-(((
>> >
>> > If can you help me I will be very very happy? :-(
>> >
>> > Sincerely yours
>> >
>> > Department of Physics, Siirt University, Siirt, Turkey
>> >
>> > --
>> > Dr.Ahmet YILDIRIM
>> >
>
>
>
> --
> Ahmet YILDIRIM
>
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Re: [gmx-users] Link to Intel MKL (fftw) via cmake options


On 30/10/2011 8:56 AM, Mirco Wahab wrote:

On 24.10.2011 23:23, Szilárd Páll wrote:

I've just realized that both you and the similar report you linked to
were using CMake 2.8.3. If you don't succeed could you try another
CMake version?


I could replicate the error with the simple cmake inviocation you 
proposed in your reply:


cmake ../gromacs-4.5.5 -DGMX_MPI=ON  
-DCMAKE_INSTALL_PREFIX=/tmp/gromacs-4.5 &&

make mdrun -j4 &&  make install-mdrun


This fails w/cmake 2.8.3 as before.

Then, I installed cmake 2.8.6 on the same system, cleaned the
build path and rerunned the build.

Your suspicion was correct, *it now works* (w/2.8.6).

So, 2.8.3 messes up the build process independend
of the specific tool chain, maybe this could be
added as a warning to the compilation instructions.


Thanks for the report. We actually do have a warning against 2.8.3 here 
http://www.gromacs.org/Developer_Zone/Cmake but I don't know if it is 
the origin of your issue.


Mark



BTW, I even managed to get an win64 (multithreaded,
non-MPI) executeable displaying respectable performance
by using  windows-cmake, visual studio 2010 SP1,
visual studio sdk SP1 7.1/64, and Nasm-win.

Thank you very much for your help.

M.


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Re: [gmx-users] position restraints on heavy atoms or all?


On 30/10/2011 11:04 AM, Yun Shi wrote:

Hello all,

I am using amber99SB to model an antibody with organic ligands.

I know we could choose to restrain all atoms or only heavy atoms 
during the equilibration. But I wonder if this really matters for my 
system. As far as I know, equilibration is aimed at getting the 
temperature and pressure right, mainly for the solvent. And as long as 
we are going to do a 'real' MD production run without restraints, it 
should not matter too much how we restrained the antibody and ligands?


Initial velocities are sampled from a theoretical distribution. Initial 
positions can be quite unphysical from whatever process created them - 
particularly hydrogen atoms. These can combine poorly in the absence of 
some sensible restraints. Only you can assess the quality of your input 
model.


Mark



I am not if I am right about this. Any suggestions?

Thanks,
Yun




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[gmx-users] Adding Hydrogens by pdb2gmx

Dear Gromacs Users!

I could not find how I can add missing hydrogens after their removing by
pdb2gmx -ignh.

I have modified structure of my protein after editing by some soft and I
removed all hydrogens but now I want to add it back in accordance with
gromos ff topology

How I can do it ?

James
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[gmx-users] Re: Structure preparation for the simulation

> Dear Gromacs Users!
>
>
> I'd like to know about external software wich could be used for structure
> processing for the futher simulation in Gromacs. Today I've tried one of the
> most popular such software Amber tools but I've forced with problems during
> compilation of it ") So I'm looking for possible analogues )
>
> First of all I'm intresting in software for the addition different CAPing
> groups to N and C termi of my protein.
>
> Is there any plugins for Pymol or VMD for such purposes? I've loked for this
> option in both of that software but couldnot  find
>
>
> Thank you for your help,
>
> James

Among free solutions... maybe this would help:
http://www.chemaxon.com/marvin/sketch/index.php

I don't know molecular editor plugins for VMD, but it would be cool,
if one is accessible.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] Number of nodes




Kavyashree M wrote:

Dear Users,

I was trying to run a simulation (gromacs4.5.3)
on a Bluegene/L machine. But I was unable to run.
System admin say that I need to change the input
file. I am not sure what needs to be changed in the
input file which specifies no. of nodes usage.



Sounds like your system admin should be offering you some more help, since they 
know the specifics of the hardware, queuing software, etc.



I am not familiar with the bluegene machines. Kindly
suggest the possible solutions.



Without seeing your input file(s), there's nothing anyone can do.  Be mindful 
that this list pertains to Gromacs-specific problems, which do not seem to be 
present here.


-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] Adding Hydrogens by pdb2gmx




James Starlight wrote:

Dear Gromacs Users!

I could not find how I can add missing hydrogens after their removing by 
pdb2gmx -ignh.


I have modified structure of my protein after editing by some soft and I 
removed all hydrogens but now I want to add it back in accordance with 
gromos ff topology


How I can do it ?



They are removed and rebuilt entirely by pdb2gmx in accordance with the 
instructions found in the .hdb file.  If there are no hydrogens in the input, 
then -ignh is irrelevant.


-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] Adding Hydrogens by pdb2gmx

Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh
with gromos force field

I've checked conf.gro by VMD and this structure didnt contains any
hydrogens ;o

James

2011/10/31 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>> I could not find how I can add missing hydrogens after their removing by
>> pdb2gmx -ignh.
>>
>> I have modified structure of my protein after editing by some soft and I
>> removed all hydrogens but now I want to add it back in accordance with
>> gromos ff topology
>>
>> How I can do it ?
>>
>>
> They are removed and rebuilt entirely by pdb2gmx in accordance with the
> instructions found in the .hdb file.  If there are no hydrogens in the
> input, then -ignh is irrelevant.
>
> -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] Adding Hydrogens by pdb2gmx




James Starlight wrote:
Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro 
-ignh  with gromos force field


I've checked conf.gro by VMD and this structure didnt contains any 
hydrogens ;o




I highly doubt that.  I've used one of the Gromos96 force fields for nearly all 
of my work and it has never failed in any Gromacs version.  Perhaps you're 
simply not taking into account the fact that Gromos96 parameter sets are united 
atom, meaning that aliphatic hydrogens are not represented explicitly.


-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] Number of nodes

2011-10-31 Thread Kavyashree M

Hello,

System Admin said that the Job fails on 32 and 128 because memory
is insufficient for each task, so upon increasing the nodes, data gets
distributed across more number of nodes and each node gets less
memory occupancy and he also mentioned that he was able to run
on 512 nodes but it was giving error for not having sufficient data for
512 nodes.

I have run the same job on 8 nodes in i7 machine.

Thank you
With Regards
Kavya

On Mon, Oct 31, 2011 at 5:47 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear Users,
>>
>> I was trying to run a simulation (gromacs4.5.3)
>> on a Bluegene/L machine. But I was unable to run.
>> System admin say that I need to change the input
>> file. I am not sure what needs to be changed in the
>> input file which specifies no. of nodes usage.
>>
>>
> Sounds like your system admin should be offering you some more help, since
> they know the specifics of the hardware, queuing software, etc.
>
>
>  I am not familiar with the bluegene machines. Kindly
>> suggest the possible solutions.
>>
>>
> Without seeing your input file(s), there's nothing anyone can do.  Be
> mindful that this list pertains to Gromacs-specific problems, which do not
> seem to be present here.
>
> -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
>
> ==**==
> --
> 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/Searchbefore
>  posting!
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> Can't post? Read 
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Re: [gmx-users] Number of nodes


On 31/10/2011 11:29 PM, Kavyashree M wrote:

Hello,

System Admin said that the Job fails on 32 and 128 because memory
is insufficient for each task, so upon increasing the nodes, data gets
distributed across more number of nodes and each node gets less
memory occupancy and he also mentioned that he was able to run
on 512 nodes but it was giving error for not having sufficient data for
512 nodes.


That combination of observations is inconceivable. 60K atom simulations 
run just fine on 32 nodes in coprocessor or virtual-node mode, and I'd 
bet 600K atoms is also fine.




I have run the same job on 8 nodes in i7 machine.


A very rough rule of thumb is that at least about a thousand atoms per 
processor is enough to make that number of processors worth using.


Mark



Thank you
With Regards
Kavya

On Mon, Oct 31, 2011 at 5:47 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Dear Users,

I was trying to run a simulation (gromacs4.5.3)
on a Bluegene/L machine. But I was unable to run.
System admin say that I need to change the input
file. I am not sure what needs to be changed in the
input file which specifies no. of nodes usage.


Sounds like your system admin should be offering you some more
help, since they know the specifics of the hardware, queuing
software, etc.


I am not familiar with the bluegene machines. Kindly
suggest the possible solutions.


Without seeing your input file(s), there's nothing anyone can do.
 Be mindful that this list pertains to Gromacs-specific problems,
which do not seem to be present here.

-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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[gmx-users] Mismatching in Bergers DMPC bilayer lipid topology

2011-10-31 Thread chris . neale


Dear James:

Next time, please specify exactly what you did in enough detail for  
somebody else to reproduce it, much as in a manuscript. e.g. there is  
no "dmpc.gro" in that website. I can guess what you did, but that is  
not ideal.


I took a look at the files that I suppose you used and the atom names  
do appear to be mis-matched between the structure and the topology.  
That's is not necessarily a problem though. What happens if you set  
maxwarn to a large value during grompp and do a short mdrun? If that  
succeeds and looks normal, then I'd suggest to draw the structure of  
the lipid (about 50 atoms) and check out the topology by copying the  
names/charges/etc. onto your map.


I, for one, have used the dmpc.itp from that website and found that it  
is ok. I accessed the file years ago, so there is no guarantee it's  
the same file, but my topology also has names like NTM. I never did  
use that DMPC structure file though.


Chris.


-- original message --

Is here anobody who worked with the dmpc bilayers obtained from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies


I've used this bilayers with the dmpc.itp and gromos96 ff with Berger lipids
and during loading my bilayer.gro in the grompt I've obtained warning about
mismatching in some atoms in .gro relatively .itp


Warning: atom name 1 in topol_dmpc.top and dmpc.gro does not match (CN1 -
CA)
Warning: atom name 2 in topol_dmpc.top and dmpc.gro does not match (CN2 -
CB)
Warning: atom name 3 in topol_dmpc.top and dmpc.gro does not match (CN3 -
CC)
Warning: atom name 4 in topol_dmpc.top and dmpc.gro does not match (NTM - N)
Warning: atom name 5 in topol_dmpc.top and dmpc.gro does not match (CA - CD)
Warning: atom name 6 in topol_dmpc.top and dmpc.gro does not match (CB - CE)
Warning: atom name 12 in topol_dmpc.top and dmpc.gro does not match (CC -
CF)
Warning: atom name 13 in topol_dmpc.top and dmpc.gro does not match (CD -
CG)
Warning: atom name 30 in topol_dmpc.top and dmpc.gro does not match (CE -
CH)
Warning: atom name 47 in topol_dmpc.top and dmpc.gro does not match (CN1 -
CA)
Warning: atom name 48 in topol_dmpc.top and dmpc.gro does not match (CN2 -
CB)
Warning: atom name 49 in topol_dmpc.top and dmpc.gro does not match (CN3 -
CC)
Warning: atom name 50 in topol_dmpc.top and dmpc.gro does not match (NTM -
N)
Warning: atom name 51 in topol_dmpc.top and dmpc.gro does not match (CA -
CD)
Warning: atom name 52 in topol_dmpc.top and dmpc.gro does not match (CB -
CE)
Warning: atom name 58 in topol_dmpc.top and dmpc.gro does not match (CC -
CF)
Warning: atom name 59 in topol_dmpc.top and dmpc.gro does not match (CD -
CG)
Warning: atom name 76 in topol_dmpc.top and dmpc.gro does not match (CE -
CH)
Warning: atom name 93 in topol_dmpc.top and dmpc.gro does not match (CN1 -
CA)
Warning: atom name 94 in topol_dmpc.top and dmpc.gro does not match (CN2 -
CB)
(more than 20 non-matching atom names)

Does this warning harmfull ? :)

JAmes
-

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Re: [gmx-users] Adding Hydrogens by pdb2gmx

exactly

all hydrogens were represented as a part of the groupd in wich they were.
So is there possible way to explicit it?

Another question about pdb2gmx. about -term
as I understood this must be used only if atoms for CAP groups are
presented in the PDB file mustnt it?
So what term exactly do? Doest it make a connection beetween CAP and C and
N termi or anothing else?


James

2011/10/31 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh
>>  with gromos force field
>>
>> I've checked conf.gro by VMD and this structure didnt contains any
>> hydrogens ;o
>>
>>
> I highly doubt that.  I've used one of the Gromos96 force fields for
> nearly all of my work and it has never failed in any Gromacs version.
>  Perhaps you're simply not taking into account the fact that Gromos96
> parameter sets are united atom, meaning that aliphatic hydrogens are not
> represented explicitly.
>
>
> -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] Adding Hydrogens by pdb2gmx




James Starlight wrote:

exactly

all hydrogens were represented as a part of the groupd in wich they 
were. So is there possible way to explicit it?




I'm not quite sure I follow.  A united atom force field, by definition, does not 
have aliphatic hydrogens.  I suggest you consult the literature and understand 
the intrinsics of the chosen force field before you attempt to use it.



Another question about pdb2gmx. about -term
as I understood this must be used only if atoms for CAP groups are 
presented in the PDB file mustnt it?


The -ter option can be useful in changing the protonation state of the termini 
or in adding caps.


So what term exactly do? Doest it make a connection beetween CAP and C 
and N termi or anothing else?




By default, pdb2gmx builds charged termini (NH3+ and COO-), per the typical 
protonation states of these groups in aqueous solution.  If a cap is present, 
then you don't want pdb2gmx doing that, so by choosing "None" for the termini in 
conjunction with the caps, only one proton is added to the N-terminus (as in an 
amide), and only one carbonyl oxygen remains on the C-terminus, such that the 
caps can be added in a sensible way.


-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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[gmx-users] Re: Prosessing of the pre-eqilibrated lipid bilayer

So does anobody know possible sollution for the reduce size of the existing
bilayer?
E.g I've preequilibrated 128 lipids in bilayer and want to obtain 32 lipid
bilayer and dont perturb overall topology of the system
In my lab there is only extremely weak CPU. it could not make md for large
systems ;p

James
2011/10/30 James Starlight 

> Dear Gromacs Users!
>
> I wounder to know about possible algorithm of preparation of the existing
> lipid bilayer for further simulation.
> E.g I have some pre-equilibrated bilayer consisted of symmetrical lipid
> organization. Now I'd like to remove some lipids from the edges of my
> bilayer to reduce overall ammounts lipids but dont perturb symmetry of the
> system. Then I'd like to place this bilayer to the rombic box (
> corresponded to the organzation of the new bilayer system).
> How I could to realise such operation of the lipid removing ?
>
> In addition I'd like to check Area per lipid value during that removing.
> How this could be done?
>
> James
>
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Re: [gmx-users] Simulation of membrane protein

In some papers I found Gromacs graphs showed indirectly measurements of the
time evolution of the Area per lipid value. What gromac's program could be
used for it for cheacking the above value during simulation runs ?

JAmes

2011/10/29 James Starlight 

> It's appeared new question about G_membed
>
> Does anobody used this algorithm for insertion of their proteins ?
> In particular I wounder to know how I can to find optimal parameters (
> different scaling factors like in the below command) for insertion in my
> system( single alpha helix in DMPC bilayer system) and how I can measure
> area per lipid in the output system?
>
>g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
> -zinit 1.1 -zend 1.0 -nz 100
>
>
> James
>
>
> 2011/10/25 Justin A. Lemkul 
>
>>
>>
>> James Starlight wrote:
>>
>>> Justin,
>>>
>>> I've found the same task of MSU's students :) They simulate membrane
>>> formation without NPT stage ( after NVT they run production MD). From they
>>> reports I've found that simplest membrane system could be formed within
>>> 10-30 Ns.  But what about try to make such simulation in vacuum at first
>>> without any water ? Might the bilayer been formed in such conditions?
>>>
>>> Finally I have small question about pereodic boundaries of such bilayer
>>> system.
>>>
>>> E.g I've done simplest system with water consisted of 8 lipid molecules
>>> + some water.
>>> This is the representation of the system http://i1209.photobucket.com/**
>>> albums/cc394/own11/lipids8.png
>>> I want to simulate bilayer formation as well as concomitant hydrophobic
>>> effect ( removing all water from formed bilayer)
>>> Does the PBC presented in that example ( 2.64196   2.64196   6.85002 for
>>> 8 lipids) are enought for such lipid movement? It seems that more free
>>> space aree needed for overal turn of lipid molecules. How I can calculate
>>> exactly  PBC value required for my system ?
>>>
>>>
>> I agree that your system has insufficient space for any real movement
>> without violating the minimum image convention.  Your system must have
>> adequate room for any lipid to rotate in any direction, and be of
>> sufficient size to accommodate a formed membrane, which will have
>> dimensions dictated by the APL for the chosen lipid (and of course, the
>> force field's ability to produce that value).
>>
>>
>> -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
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>> Support/Mailing_Lists/Searchbefore
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>
>
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[gmx-users] LINCS crushes

2011-10-31 Thread Yuri Garmay

Hi, all!

I am trying to simulate a system of peptide, water, NaCl and DMSO.
I used pdb2gmx to generate .top file for DMSO and then created this .itp:
(initial DMSO structure had been minimized before it was used for box
generation)

[ moleculetype ]
; Namenrexcl
DMSO   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
; residue   1 DMSO rtp DMSO q  0.0
 1  SDmso  1   DMSO  SDmso  10.12753  32.06   ;
qtot 0.1275
 2  ODmso  1   DMSO  ODmso  1   -0.4475315.9994   ;
qtot -0.32
 3  CDmso  1   DMSO  CDms1  1   0.16 15.035   ;
qtot -0.16
 4  CDmso  1   DMSO  CDms2  1   0.16 15.035   ;
qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
1 2 2gb_41
1 3 2gb_42
1 4 2gb_42
2 3 2gb_49
2 4 2gb_49
3 4 2gb_50

Corresponding record in /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
is:

[ DMSO ]
 [ atoms ]
SDmso SDmso 0.12753 0
ODmso ODmso-0.44753 0
CDms1 CDmso 0.16000 0
CDms2 CDmso 0.16000 0
 [ bonds ]
SDmso ODmsogb_41
SDmso CDms1gb_42
SDmso CDms2gb_42
ODmso CDms1gb_49
ODmso CDms2gb_49
CDms1 CDms2gb_50
 [ angles ]
;  aiajak   gromos type
 [ impropers ]
;  aiajakal   gromos type
 [ dihedrals ]
;  aiajakal   gromos type

Then I created box with genbox using -ci and -cs options. I did add
following strings in system .top file:
before [ system ]

; Include DMSO topology
#include "dmso.itp"

after [ molecules ]

DMSO 69

Parameters what I used for energy minimization was:

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)

; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme

constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

Then I get minimization crushed after such warnings:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.646692, max 1.998582 (between atoms 237 and 236)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
223222  148.10.1535   0.0548  0.1530

When I set constraints = h-bonds minimization was successful.

It seems LINCS algorithm has limitations on the molecule topology. I didn't
know details of this method and need help.
What should I do for simulation works? Is there need to change DMSO
topology or maybe it is better to use constraints = h-bonds option?

Regards,
Yuri.
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Re: [gmx-users] Simulation of membrane protein




James Starlight wrote:


In some papers I found Gromacs graphs showed indirectly measurements of 
the time evolution of the Area per lipid value. What gromac's program 
could be used for it for cheacking the above value during simulation runs ?




There is no Gromacs tool for this.  For a simple membrane system, one can use 
g_energy to extract box vectors over time, which can then be divided by the 
number of lipids per leaflet to extract the APL.  For systems with proteins 
embedded in membranes, it is no trivial exercise to make such measurements.  We 
wrote a program several years ago that calculates APL for such systems:


http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

The program can only be run on single snapshots at the moment, but you can 
assemble time evolution from the output.


-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] LINCS crushes




Yuri Garmay wrote:

Hi, all!

I am trying to simulate a system of peptide, water, NaCl and DMSO.
I used pdb2gmx to generate .top file for DMSO and then created this .itp:
(initial DMSO structure had been minimized before it was used for box 
generation)


[ moleculetype ]
; Namenrexcl
DMSO   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass 
 typeBchargeB  massB

; residue   1 DMSO rtp DMSO q  0.0
 1  SDmso  1   DMSO  SDmso  10.12753  32.06   ; 
qtot 0.1275
 2  ODmso  1   DMSO  ODmso  1   -0.4475315.9994   ; 
qtot -0.32
 3  CDmso  1   DMSO  CDms1  1   0.16 15.035   ; 
qtot -0.16
 4  CDmso  1   DMSO  CDms2  1   0.16 15.035   ; 
qtot 0


[ bonds ]
;  aiaj functc0c1c2c3
1 2 2gb_41
1 3 2gb_42
1 4 2gb_42
2 3 2gb_49
2 4 2gb_49
3 4 2gb_50

Corresponding record 
in /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp is:


[ DMSO ]
 [ atoms ]
SDmso SDmso 0.12753 0
ODmso ODmso-0.44753 0
CDms1 CDmso 0.16000 0
CDms2 CDmso 0.16000 0
 [ bonds ]
SDmso ODmsogb_41   
SDmso CDms1gb_42   
SDmso CDms2gb_42   
ODmso CDms1gb_49   
ODmso CDms2gb_49   
CDms1 CDms2gb_50   
 [ angles ]

;  aiajak   gromos type
 [ impropers ]
;  aiajakal   gromos type
 [ dihedrals ]
;  aiajakal   gromos type

Then I created box with genbox using -ci and -cs options. I did add 
following strings in system .top file:

before [ system ]

; Include DMSO topology
#include "dmso.itp"

after [ molecules ]

DMSO 69

Parameters what I used for energy minimization was:

; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions

nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)

; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme

constraint_algorithm = lincs ; holonomic constraints 
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained

lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

Then I get minimization crushed after such warnings:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.646692, max 1.998582 (between atoms 237 and 236)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
223222  148.10.1535   0.0548  0.1530

When I set constraints = h-bonds minimization was successful.

It seems LINCS algorithm has limitations on the molecule topology. I 
didn't know details of this method and need help.


LINCS is actually quite stable, but will crash if the system is not ;)

What should I do for simulation works? Is there need to change DMSO 
topology or maybe it is better to use constraints = h-bonds option?




Try minimizing again now with all bonds constrained using the output of the EM 
that ran.  Generally, if EM crashes, your system contains some unresolvable 
clash or inappropriate geometry.  Perhaps you have now relaxed the bad 
interactions sufficiently to proceed.


-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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[gmx-users] Re: Re: Re: Reference structure for g_covar

2011-10-31 Thread vivek modi

Hi Tsjerk,

Thanks for your earlier reply. It makes things clear.

Is it possible that the cosine content of  first PC is high because of the
fluctuations in the long loop  regions which dominate and not in the
secondary structures. The fluctuations in the loop regions is of no
interest to me and I suspect it is making the cosine content high.  If I
repeat the calculations by selecting only the secondary structures (helices
in this protein) and ignoring the loop regions, then the cosine content is
fairly low. As I have a good understanding of the system I am working on I
know that loops do not play any role.

Is it appropriate then to perform PCA by selecting only the secondary
structure elements and not loops. What do you suggest ?


Regards,

-Vivek



 Message: 2
> Date: Thu, 20 Oct 2011 18:22:53 +0200
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Re: Re: Reference structure for g_covar
> To: Discussion list for GROMACS users 
> Message-ID:
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Vivek,
>
> The high cosine content of the first pc indicates that the system is still
> equilibrating. You're sort of still on the road from A (the starting
> position) to B (the equilibrated state).
>
> Hope it helps,
>
> Tsjerk
>
> On Oct 20, 2011 5:07 PM, "vivek modi"  wrote:
>
> Hi Tsjerk,
>
> Thanks a lot for your reply.
> But now I will ask a very naive  question.
>
> My study involves understanding the dynamics of a group of closely related
> proteins. All of them are simulated for a period of 100ns each.
> I have also analyzed the RMSD using g_rms for all of them and it  becomes
> very stable after 20-30ns for all the proteins.
> But when I do PCA I see high cosines (~0.8) for the first PC. For all the
> other PCs the cosine content is very low.
>
> The question is  that is it appropriate to ignore the first PC and make
> inference about the motion of the protein by using other PCs ?
>
>
> Thanks a lot.
>
>
> Regards,
>
> -Vivek Modi
>
> Date: Wed, 19 Oct 2011 13:58:00 +0200
> > From: Tsjerk Wassenaar 
> > Subject: Re: [gmx-users] Reference structure for g_covar
> > To: Discussion list for GROMACS users 
> > Message-ID:
> > n78nwo+o0utm7ovdwz4hbgjeylj8x0nbwewwlz...@mail.gmail.com
> > >
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > > > Hi Vivek, > > I explained related matters in some detail on this list
> > earlier, and > would urge...
> >
>
>
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[gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Sanku M

Hi,
  I have done some steered MD simulation and I want to construct the potential 
of mean force from these pull-profile using Jarzinsky's inequality. I wanted to 
see whether, in updated version of gromacs, there is any implementation of  
extracting PMF from SMD simulations. 
If not, can anyone suggest some guidelines how to do it.
Sanku-- 
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Re: [gmx-users] Simulation of membrane protein

Thanks, Justin
I'll test your program soon.

Today also I have some problems with generation of the posre for lipids

I have lipid bilayer in pdb. Then I selected one lipid molecule and move it
to  separate pdb and convert it to gro via editconf.
Than I've used genres and generate posre file for 1 lipid. Than I include
tis posre to topology of my bilayer
using gropt I obtain eror that I'm using wrong posre topology

Also I've tried to include posre.itp to my lipid.itp ( this file contain
link to posre on default) This run didnt produce any errors but as the
result posres have not been worked ( I obtained perturbed bilayer after
minimization)

How I can generate work posre for my bilayer to prevent perturbation after
equilibration or minimization ?

James

2011/10/31 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>>
>> In some papers I found Gromacs graphs showed indirectly measurements of
>> the time evolution of the Area per lipid value. What gromac's program could
>> be used for it for cheacking the above value during simulation runs ?
>>
>>
> There is no Gromacs tool for this.  For a simple membrane system, one can
> use g_energy to extract box vectors over time, which can then be divided by
> the number of lipids per leaflet to extract the APL.  For systems with
> proteins embedded in membranes, it is no trivial exercise to make such
> measurements.  We wrote a program several years ago that calculates APL for
> such systems:
>
> http://www.bevanlab.biochem.**vt.edu/GridMAT-MD/
>
> The program can only be run on single snapshots at the moment, but you can
> assemble time evolution from the output.
>
>
> -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] Simulation of membrane protein




James Starlight wrote:

Thanks, Justin
I'll test your program soon.

Today also I have some problems with generation of the posre for lipids

I have lipid bilayer in pdb. Then I selected one lipid molecule and move 
it to  separate pdb and convert it to gro via editconf.
Than I've used genres and generate posre file for 1 lipid. Than I 
include tis posre to topology of my bilayer

using gropt I obtain eror that I'm using wrong posre topology

Also I've tried to include posre.itp to my lipid.itp ( this file contain 
link to posre on default) This run didnt produce any errors but as the 
result posres have not been worked ( I obtained perturbed bilayer after 
minimization)


How I can generate work posre for my bilayer to prevent perturbation 
after equilibration or minimization ?




Since posre.itp is the default name given to the protein position restraint file 
by pdb2gmx, the first step is to use a different name.  Then, you have to add 
the new #include statement in the correct location in the topology.  Presuming 
you do that, the lipids should be restrained in whatever manner you've specified.


-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] Simulation of membrane protein

I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )


I've included this in the topology of the bilayer

; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

; Include ion topologies
#include "gromos53a6_lipid.ff/ions.itp"

#ifdef POSRES_LIPID
#include "posre_lipid.itp"
#endif

; System specifications
[ system ]
128-Lipid DMPC Bilayer in water

[ molecules ]
; molecule name nr.
DPPC 64
SOL  1193
SOL   690


Also I've tried to make posre for whole system ( large posres ) but it also
was finished with same error

Fatal error:
[ file posre_lipid.itp, line 6 ]:
Atom index (2) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What's most true for such multy system. Generate posre only for 1 part or
for whole system?

James

2011/10/31 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Thanks, Justin
>> I'll test your program soon.
>>
>> Today also I have some problems with generation of the posre for lipids
>>
>> I have lipid bilayer in pdb. Then I selected one lipid molecule and move
>> it to  separate pdb and convert it to gro via editconf.
>> Than I've used genres and generate posre file for 1 lipid. Than I include
>> tis posre to topology of my bilayer
>> using gropt I obtain eror that I'm using wrong posre topology
>>
>> Also I've tried to include posre.itp to my lipid.itp ( this file contain
>> link to posre on default) This run didnt produce any errors but as the
>> result posres have not been worked ( I obtained perturbed bilayer after
>> minimization)
>>
>> How I can generate work posre for my bilayer to prevent perturbation
>> after equilibration or minimization ?
>>
>>
> Since posre.itp is the default name given to the protein position
> restraint file by pdb2gmx, the first step is to use a different name.
>  Then, you have to add the new #include statement in the correct location
> in the topology.  Presuming you do that, the lipids should be restrained in
> whatever manner you've specified.
>
>
> -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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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
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Re: [gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Laura Kingsley

There is a way to extract the PMF from sMD simulations using the 
weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's 
tutorial does a nice job of explaining it:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

- Laura



On 10/31/2011 11:05 AM, Sanku M wrote:

Hi,
  I have done some steered MD simulation and I want to construct the 
potential of mean force from these pull-profile using Jarzinsky's 
inequality. I wanted to see whether, in updated version of gromacs, 
there is any implementation of  extracting PMF from SMD simulations.

If not, can anyone suggest some guidelines how to do it.
Sanku


--
Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643

-- 
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Re: [gmx-users] Simulation of membrane protein


On 1/11/2011 3:00 AM, James Starlight wrote:

I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )


I've included this in the topology of the bilayer

; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

; Include ion topologies
#include "gromos53a6_lipid.ff/ions.itp"

#ifdef POSRES_LIPID
#include "posre_lipid.itp"
#endif

; System specifications
[ system ]
128-Lipid DMPC Bilayer in water

[ molecules ]
; molecule name nr.
DPPC 64
SOL  1193
SOL   690


Also I've tried to make posre for whole system ( large posres ) but it 
also was finished with same error


Fatal error:
[ file posre_lipid.itp, line 6 ]:
Atom index (2) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section 
"position_restraints"

in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors


The text of the error is exactly right about what is wrong. Please read 
and take time to understand before firing off email. You will learn more 
and faster if you read and understand documentation relevant to a 
situation before asking questions, and you will use less of everyone 
else's volunteer time. Also, if you follow that link, you will find a 
worked example of fixing your problem.




What's most true for such multy system. Generate posre only for 1 part 
or for whole system?


It is often more profitable to understand why the error occurs, rather 
than guess at the form of the solution.


Mark



James

2011/10/31 Justin A. Lemkul mailto:jalem...@vt.edu>>



James Starlight wrote:

Thanks, Justin
I'll test your program soon.

Today also I have some problems with generation of the posre
for lipids

I have lipid bilayer in pdb. Then I selected one lipid
molecule and move it to  separate pdb and convert it to gro
via editconf.
Than I've used genres and generate posre file for 1 lipid.
Than I include tis posre to topology of my bilayer
using gropt I obtain eror that I'm using wrong posre topology

Also I've tried to include posre.itp to my lipid.itp ( this
file contain link to posre on default) This run didnt produce
any errors but as the result posres have not been worked ( I
obtained perturbed bilayer after minimization)

How I can generate work posre for my bilayer to prevent
perturbation after equilibration or minimization ?


Since posre.itp is the default name given to the protein position
restraint file by pdb2gmx, the first step is to use a different
name.  Then, you have to add the new #include statement in the
correct location in the topology.  Presuming you do that, the
lipids should be restrained in whatever manner you've specified.


-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] Simulation of membrane protein

James Starlight wrote:

I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )

I've included this in the topology of the bilayer

; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

; Include ion topologies
#include "gromos53a6_lipid.ff/ions.itp"

#ifdef POSRES_LIPID
#include "posre_lipid.itp"
#endif

; System specifications
[ system ]
128-Lipid DMPC Bilayer in water

[ molecules ]
; molecule name nr.
DPPC 64
SOL 1193
SOL 690

Also I've tried to make posre for whole system ( large posres ) but it
also was finished with same error

Fatal error:
[ file posre_lipid.itp, line 6 ]:
Atom index (2) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
"position_restraints"

in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What's most true for such multy system. Generate posre only for 1 part
or for whole system?

Position restraints can only be applied on a [moleculetype] basis. Thus, order
matters a lot, and the whole system cannot be restrained in one file. See the
example here:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

As it stands now, the topology you've shown tries to apply lipid position
restraints after the ions have been #included, which makes no sense at all.

-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] LINCS crushes

2011-10-31 Thread Yuri Garmay

>
> Try minimizing again now with all bonds constrained using the output of
> the EM that ran.  Generally, if EM crashes, your system contains some
> unresolvable clash or inappropriate geometry.  Perhaps you have now relaxed
> the bad interactions sufficiently to proceed.
>


I had examined structure before first minimization and if it was cause I
would have been wondered. However I have tried that advice, but this didn't
solve the problem. Minimization didn't crush, but didn't lead to any
significant atom position changes too. NPT
position restrained simulation with all bonds constrained crushes with
minimized structure, but the same with hbonds constrained doesn't. The
former produces exploded DMSO structures, the latter produces visually
correct trajectory. So, It seems that structure is not the matter.

--
Regards,
Yuri
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Re: [gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Sanku M

Hi Laura,
  I do not think Justin Lemkul's tutorial is suggesting extracting PMF using 
SMD simulation. What is does that it uses SMD to generate the initial 
configurations for different windows and then perform umbrella sampling 
separately on each windows to subsequently extract the PMF using WHAM based on 
the data set on umbrella sampling.

Sanku



From: Laura Kingsley 
To: gmx-users@gromacs.org
Sent: Monday, October 31, 2011 11:09 AM
Subject: Re: [gmx-users] Jarzinsky's inequality from SMD simulation


There is a way to extract the PMF from sMD simulations using the weighted 
histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a 
nice job of explaining it:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

- Laura



On 10/31/2011 11:05 AM, Sanku M wrote: 
Hi,
>  I have done some steered MD simulation and I want to construct the potential 
>of mean force from these pull-profile using Jarzinsky's inequality. I wanted 
>to see whether, in updated version of gromacs, there is any implementation of  
>extracting PMF from SMD simulations. 
>If not, can anyone suggest some guidelines how to do it.
>Sanku

-- 
Laura Kingsley Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University 
Office: RHPH 504A 
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643
-- 
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Re: [gmx-users] Jarzinsky's inequality from SMD simulation

2011-10-31 Thread Laura Kingsley

Yes, I believe that is correct. I know that this is one way to get the 
PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky 
equation explicitly to extract the PMF from just a sMD run with Gromacs.


On 10/31/2011 01:29 PM, Sanku M wrote:
using SMD simulation. What is does that it uses SMD to generate the 
initial configurations for different windows and then perform umbrella 
sampling separately on each windows to subsequently extract the PMF 
using WHAM based on the data set on umbrella sampling.


--
Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643

--
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Re: [gmx-users] Jarzinsky's inequality from SMD simulation




Laura Kingsley wrote:
Yes, I believe that is correct. I know that this is one way to get the 
PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky 
equation explicitly to extract the PMF from just a sMD run with Gromacs.




One approach:

http://lists.gromacs.org/pipermail/gmx-users/2011-August/063477.html

I've never tried it, so I don't know if that is correct or not.  Go to 
http://www.gromacs.org/Support/Mailing_Lists/Search and search for "Jarzynski" 
and you will pull up more on this topic.


-Justin


On 10/31/2011 01:29 PM, Sanku M wrote:
using SMD simulation. What is does that it uses SMD to generate the 
initial configurations for different windows and then perform umbrella 
sampling separately on each windows to subsequently extract the PMF 
using WHAM based on the data set on umbrella sampling.




--


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] Re: how to calculate the force between two groups (Mark Abraham)

2011-10-31 Thread Tom

Thanks Mark!

It was actually what I did.
mdrun -rerun  with well-chosen energy group exclusions only gives the
energy
between certain pairs of group, not the forces.

g_traj gives the overall forces not the force between certain pair.

Thanks a lot for any further idea to obtain the force for certain pair of
groups!

Tom

On 31/10/2011 4:05 AM, Tom wrote:
> Dear Gromacs Users,
>
> I have a question about how to ouput the force between two groups.
>
> Suppose the system consists of the groups: A, B, C and D.
> I need the force only between the groups A and B.
>
> g_traj looks only to be able to report the overal forces and cann not
distiguish
> the forces from different groups.
>
> Is there any cunning way to do it.
>
mdrun -rerun  with well-chosen energy group exclusions probably works
for you.

Mark
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[gmx-users] gromacs query

2011-10-31 Thread Anushree Tripathi

I m using gromacs 4.5.3 version and trying to simulate a protein in liquid
media but I found problem in eqilibration step especially when I give
following command:

mdrun -deffnm nvt

.After giving this command it is showing error,i.e.,
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 9.02659 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition.
What should I do now.Please suggest me.I tried above options also.
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Re: [gmx-users] gromacs query

Anushree Tripathi wrote:
I m using gromacs 4.5.3 version and trying to simulate a protein in
liquid media but I found problem in eqilibration step especially when I
give following command:

mdrun -deffnm nvt

.After giving this command it is showing error,i.e.,
There is no domain decomposition for 4 nodes that is compatible with the given
box and a minimum cell size of 9.02659 nm
Change the number of nodes or mdrun option -rdd or -dds

Look in the log file for details on the domain decomposition.
What should I do now.Please suggest me.I tried above options also.

I don't see any reason why a normal protein in water simulation should require
such a huge minimum cell size. See here for more:

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

Likely you have something wrong in the topology, .mdp file, or both.

-Justin

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Re: [gmx-users] Re: Structure preparation for the simulation

2011-10-31 Thread Itamar Kass

Hi James,

I usually use Swiss-PdbViewer (http://spdbv.vital-it.ch/disclaim.html). Despite 
being an old and not well supported for any system, it is still a free and easy 
to use and allows the building and mutating of residues  in addition to 
automatically adding missing atoms. 

You can just build an extra GLY at the end of the your chain and using text 
editor change it to N/C-caps.


Cheers,
Itamar

On 31/10/2011, at 11:16 PM, Dr. Vitaly V. Chaban wrote:

>> Dear Gromacs Users!
>> 
>> 
>> I'd like to know about external software wich could be used for structure
>> processing for the futher simulation in Gromacs. Today I've tried one of the
>> most popular such software Amber tools but I've forced with problems during
>> compilation of it ") So I'm looking for possible analogues )
>> 
>> First of all I'm intresting in software for the addition different CAPing
>> groups to N and C termi of my protein.
>> 
>> Is there any plugins for Pymol or VMD for such purposes? I've loked for this
>> option in both of that software but couldnot  find
>> 
>> 
>> Thank you for your help,
>> 
>> James
> 
> Among free solutions... maybe this would help:
> http://www.chemaxon.com/marvin/sketch/index.php
> 
> I don't know molecular editor plugins for VMD, but it would be cool,
> if one is accessible.
> 
> -- 
> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
> Univ. Rochester, Rochester, New York 14627-0216
> THE UNITED STATES OF AMERICA
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-- 

"In theory, there is no difference between theory and practice. But, in 
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail:  itamar.k...@monash.edu




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[gmx-users] equilbium convergence and RMSD structure

2011-10-31 Thread larif sofiene

Greeting
I wonder if my MD simulation of a monomeric enzyme in WT and 3 mutated
forms has converged to equilibrium and simulation is suitable for analysis.
The 4 MD simulations are done in cubic water volume, 500 ps of steepest
descent minimization , with 100 ps of NVT ensemble and 100 ps of NPT
ensemble , reaching for all of them their desirable value and being stable
over time
When doing an MD production for 10 ns with those parameter :
* constraint_algorithm = lincs
* constraints= all-bonds
* coulombtype= PME
* tcoupl= V-rescale
* pcoupl= Parrinello-Rahman
* pcoupltype= isotropic

leading to those RMSD
http://imageshack.us/photo/my-images/840/rmsd.png/
the first one on the upper left is wild type other are mutants.
my question is are my system in equilibrium despite those 2 spikes on 7 and
9 ns in WT RMSD , knowing that all the 4 MD had stable radius of gyration ,
stable potential energy , stable H bond forming and dissociation over time
and reasonable H bonds under structural analysis, and if so, does those
spikes mean structural changes in flexible regions that i must check for
with RMSF ?
Thanks in advance for responding :)
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Re: [gmx-users] equilbium convergence and RMSD structure




larif sofiene wrote:
Greeting 
I wonder if my MD simulation of a monomeric enzyme in WT and 3 mutated 
forms has converged to equilibrium and simulation is suitable for analysis.
The 4 MD simulations are done in cubic water volume, 500 ps of steepest 
descent minimization , with 100 ps of NVT ensemble and 100 ps of NPT 
ensemble , reaching for all of them their desirable value and being 
stable over time
When doing an MD production for 10 ns with those parameter : 
* constraint_algorithm = lincs

* constraints= all-bonds
* coulombtype= PME
* tcoupl= V-rescale
* pcoupl= Parrinello-Rahman
* pcoupltype= isotropic

leading to those RMSD
http://imageshack.us/photo/my-images/840/rmsd.png/
the first one on the upper left is wild type other are mutants.
my question is are my system in equilibrium despite those 2 spikes on 7 
and 9 ns in WT RMSD , knowing that all the 4 MD had stable radius of 
gyration , stable potential energy , stable H bond forming and 
dissociation over time and reasonable H bonds under structural analysis, 
and if so, does those spikes mean structural changes in flexible regions 
that i must check for with RMSF ?

Thanks in advance for responding :)



Several general points:

1. I doubt that's the full .mdp file; in fact, it can't be.  Please do not post 
snippets of such information, post the full thing.  Details that may not strike 
you as significant can sometimes be.


2. 10 ns of time is relatively insignificant to study almost anything related to 
proteins.  You haven't stated your goals for these simulations, but I'd argue 
that you've got no more than 5 ns of usable data in some of the simulations, 
often less.


3. You cannot justify convergence of any phenomenon using a single simulation, 
especially of such short length.


4. It appears from the figure in the bottom left that the RMSD is still 
systematically trending upward, indicating that this simulation is not nearly 
done.  Block averaging will tell for sure whether or not I've passed this 
eyeball test.


-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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[gmx-users] Re: how to calculate the force between two groups (Mark Abraham)

On 1/11/2011 5:40 AM, Tom wrote:

Thanks Mark!

It was actually what I did.
mdrun -rerun  with well-chosen energy group exclusions only gives the 
energy

between certain pairs of group, not the forces.

Did you use nstfout to actually write the forces?

g_traj gives the overall forces not the force between certain pair.

mdrun computes interactions as a loop over energy groups and writes only 
a single number for each component of the force on each atom in each 
time step. You can't decompose anything after the fact.

Thanks a lot for any further idea to obtain the force for certain pair 
of groups!

One can use tpbconv and trjconv to create a matching pair of subset .tpr 
and trajectory files for mdrun -rerun, but I do not think this is necessary.

Mark

Tom

On 31/10/2011 4:05 AM, Tom wrote:
> Dear Gromacs Users,
>
> I have a question about how to ouput the force between two groups.
>
> Suppose the system consists of the groups: A, B, C and D.
> I need the force only between the groups A and B.
>
> g_traj looks only to be able to report the overal forces and cann 
not distiguish

> the forces from different groups.
>
> Is there any cunning way to do it.
>
mdrun -rerun  with well-chosen energy group exclusions probably works
for you.

Mark 

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Re: [gmx-users] LINCS crushes


On 1/11/2011 3:43 AM, Yuri Garmay wrote:



Try minimizing again now with all bonds constrained using the
output of the EM that ran.  Generally, if EM crashes, your system
contains some unresolvable clash or inappropriate geometry.
 Perhaps you have now relaxed the bad interactions sufficiently to
proceed.


I had examined structure before first minimization and if it was cause 
I would have been wondered. However I have tried that advice, but this 
didn't solve the problem. Minimization didn't crush, but didn't lead 
to any significant atom position changes too.


It often doesn't.

NPT position restrained simulation with all bonds constrained crushes 
with minimized structure, but the same with hbonds constrained doesn't.


Jumping straight to NPT is sometimes a bad idea. See 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation


The former produces exploded DMSO structures, the 
latter produces visually correct trajectory. So, It seems that 
structure is not the matter.


Your symptoms are consistent with a bad starting structure, wrong 
topology or invalid preparation protocol. Nothing can be ruled out yet.


Mark
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[gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread ram bio

Dear Gromacs users,

I have built a protein embedded in popc bilayer and executed pdb2gmx using
charmm27 ff on the system and the toplogy file was created without errors,
but when wanted to minimise the system with grompp i am getting an error as
: unknown cmap torsion between atoms 8377 8379 8381 8394 8397.

Could someone please explain me what this error mean and how to overcome
this.

thanks,

Pramod
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Re: [gmx-users] unknown cmap torsion between atoms


On 1/11/2011 1:24 PM, ram bio wrote:

Dear Gromacs users,

I have built a protein embedded in popc bilayer and executed pdb2gmx 
using charmm27 ff on the system and the toplogy file was created 
without errors, but when wanted to minimise the system with grompp i 
am getting an error as : unknown cmap torsion between atoms 8377 8379 
8381 8394 8397.


Could someone please explain me what this error mean and how to 
overcome this.


It means you are somehow using CMAP on a dihedral whose atom types do 
not have a known CMAP function - "unknown CMAP torsion". You need to do 
some detective work on those atoms and their types to work out why.


Mark
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Re: [gmx-users] unknown cmap torsion between atoms

2011-10-31 Thread ram bio

Hi Mark,

Thanks for the response.
I have built this system (protein in popc bilayer using charmm GUI) and
submitted the total built system to pdb2gmx, is this the reason for having
unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot
show any error. Cant the charmm gui built system be used in gromacs with
charmm27ff.

Out of the 134 atoms for each  popc in the structure file  few initial
atoms were not matching in the lipids.itp file under charmmff folder, so i
changed the atom names in the lipid.itp under popc section to match with
atom names in the structure file, is that could be reason?

moreover, grompp also throws error as no default U-B types along with
unknown CMAP torsion.

Could you please diagnose where the problem exists in my procedure and let
me know.

Thanks

Pramod

On Mon, Oct 31, 2011 at 9:57 PM, Mark Abraham wrote:

> On 1/11/2011 1:24 PM, ram bio wrote:
>
>> Dear Gromacs users,
>>
>> I have built a protein embedded in popc bilayer and executed pdb2gmx
>> using charmm27 ff on the system and the toplogy file was created without
>> errors, but when wanted to minimise the system with grompp i am getting an
>> error as : unknown cmap torsion between atoms 8377 8379 8381 8394 8397.
>>
>> Could someone please explain me what this error mean and how to overcome
>> this.
>>
>
> It means you are somehow using CMAP on a dihedral whose atom types do not
> have a known CMAP function - "unknown CMAP torsion". You need to do some
> detective work on those atoms and their types to work out why.
>
> Mark
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Re: [gmx-users] unknown cmap torsion between atoms


On 1/11/2011 2:16 PM, ram bio wrote:

Hi Mark,

Thanks for the response.
I have built this system (protein in popc bilayer using charmm GUI) 
and submitted the total built system to pdb2gmx, is this the reason 
for having unknown CMAP torsion while executing grompp, by the way 
pdb2gmx doesnot show any error. Cant the charmm gui built system be 
used in gromacs with charmm27ff.


I don't know. Either you, pdb2gmx or grompp has done something wrong.



Out of the 134 atoms for each  popc in the structure file  few initial 
atoms were not matching in the lipids.itp file under charmmff folder, 
so i changed the atom names in the lipid.itp under popc section to 
match with atom names in the structure file, is that could be reason?


Lipids do not use CMAP.



moreover, grompp also throws error as no default U-B types along with 
unknown CMAP torsion.


So you have some atom types for which the angle potentials are defined 
when the CMAP is not. That doesn't help find what atom types you are 
using that do not have CMAP definitions.




Could you please diagnose where the problem exists in my procedure and 
let me know.


No. I told you how to start to work out the problem and you seem to have 
ignored it :-)


Mark



Thanks

Pramod

On Mon, Oct 31, 2011 at 9:57 PM, Mark Abraham > wrote:


On 1/11/2011 1:24 PM, ram bio wrote:

Dear Gromacs users,

I have built a protein embedded in popc bilayer and executed
pdb2gmx using charmm27 ff on the system and the toplogy file
was created without errors, but when wanted to minimise the
system with grompp i am getting an error as : unknown cmap
torsion between atoms 8377 8379 8381 8394 8397.

Could someone please explain me what this error mean and how
to overcome this.


It means you are somehow using CMAP on a dihedral whose atom types
do not have a known CMAP function - "unknown CMAP torsion". You
need to do some detective work on those atoms and their types to
work out why.

Mark
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[gmx-users] xtc vs. trr file

2011-10-31 Thread Juliette N.

Dear all,

I am low on disk space and need to delete trr files. I turned on -x option
in all runs so generated xtc files as well. Just wondering if xtc files
contain less information than trr ones which make xtc have less size. Am I
going to lose any information other than velocities?

Thanks,
J.
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Re: [gmx-users] xtc vs. trr file