Re: [gmx-users] Umbrella_pull_simulation

Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns for equilibriation. The new profile.xvg is attached. How can I further improve it. Shahid Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul wr

Re: [gmx-users] Re: Interchain Disulfide Bond

On 21/02/2012 12:33 PM, jneeraj wrote: Thank you Mark for you prompt response. I tried: $pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f -o -p $grompp -f -c -p -o and it works perfectly, i.e. it correctly creates interchain disulfide bond. However, when I use charmm27

[gmx-users] Re: Interchain Disulfide Bond

Thank you Mark for you prompt response. I tried: $pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f -o -p $grompp -f -c -p -o and it works perfectly, i.e. it correctly creates interchain disulfide bond. However, when I use charmm27 force field instead of amber99sb, I g

[gmx-users] [solved] Using CHARMM force fields in Gromacs, pt. 2

@Peter C. Lai: I did like you suggested and now the two forcefields work in tandem as expected. @Mark Abraham: Thank you for the explanation. Best. Jernej Zidar On Mon, Feb 20, 2012 at 15:27, wrote: >> >>   There's no need to patch the forcefields.dat file because Gromacs >> will first loo

Re: [gmx-users] Interchain Disulfide Bond

On 21/02/2012 6:20 AM, jneeraj wrote: Hello, I am trying to perform a MD simulation of a protein consisting of two chains. These two chains are connected via single disulfide bond. These two chains are separated by TER record in the input pdb file. I am using charmm27 force-field. The steps that

Re: [gmx-users] T-coupling problem?

On 21/02/2012 8:39 AM, Talal Alotaibi wrote: Hi, I am trying to freeze the protein during equilibruim. I made the energy minimization with no freezing. but when I freeze the protein and try to do "grompp", it gives me this error: A more sound protocol for preparation for MD probably involves

Re: [gmx-users] Scaling/performance on Gromacs 4

On 21/02/2012 8:11 AM, Floris Buelens wrote: Poor scaling with MPI on many-core machines can also be due uneven job distributions across cores or jobs being wastefully swapped between cores. You might be able to fix this with some esoteric configuration options of mpirun (--bind-to-core worked

Re: [gmx-users] T-coupling problem?

Talal Alotaibi wrote: Hi, I am trying to freeze the protein during equilibruim. I made the energy minimization with no freezing. but when I freeze the protein and try to do "grompp", it gives me this error: == Fatal error: 14623 atoms are not par

[gmx-users] T-coupling problem?

Hi, I am trying to freeze the protein during equilibruim. I made the energy minimization with no freezing. but when I freeze the protein and try to do "grompp", it gives me this error: == Fatal error: 14623 atoms are not part of any of the T-Coupling gro

Re: [gmx-users] Scaling/performance on Gromacs 4

Poor scaling with MPI on many-core machines can also be due uneven job distributions across cores or jobs being wastefully swapped between cores. You might be able to fix this with some esoteric configuration options of mpirun (--bind-to-core worked for me with openMPI), but the surest option is

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:

Re: [gmx-users] Umbrella Pulling

On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >> >> >>On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul >>mailto:j

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:

Re: [gmx-users] Umbrella Pulling

On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > > >> >> On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>Dear Justin and Gmx Users, >> >>I run a pulling of my ligand away f

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plo

Re: [gmx-users] Umbrella Pulling

On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Justin and Gmx Users, >> >> I run a pulling of my ligand away from my protein with the same mdp file >> and I obtained two different plots - Force vs time (The breaking point >> occured at different tim

[gmx-users] g_analyze -ee

Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul To: dina dusti ; Discussion list for GROMACS users Sent: Monday, February 20, 2012 11:07 PM Subject: Re: [gmx-users] g_analyze -ee dina dusti wrote: > Dear Ju

Re: [gmx-users] g_analyze -ee

dina dusti wrote: Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! The warnings indicate that the error estimat

[gmx-users] Interchain Disulfide Bond

Hello, I am trying to perform a MD simulation of a protein consisting of two chains. These two chains are connected via single disulfide bond. These two chains are separated by TER record in the input pdb file. I am using charmm27 force-field. The steps that I am following are: pdb2gmx –ignh –

[gmx-users] Interchain Disulfide Bond

Hello, I am trying to perform a MD simulation of a protein consisting of two chains. These two chains are connected via single disulfide bond. These two chains are separated by TER record in the input pdb file. I am using charmm27 force-field. The steps that I am following are: pdb2gmx –ignh –ss

Re: [gmx-users] Umbrella_pull_simulation

shahid nayeem wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiff

[gmx-users] Umbrella Pulling

Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? My mdp file: title = Umbrella pulling simulati

Re: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

A quick answer to this is, there's two sets of tables based on equations I know of off hand for LJ's and calculating the other such LJ parameters from these. In one it uses the epsilon/ sigma and the other a table of either the 9-6 or the 6-12. The later two you can look up either on the Europ

[gmx-users] g_analyze -ee

Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! Thank you again from your help and excuse me from my delay for thank

Re: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

On 21/02/2012 4:36 AM, Lara Bunte wrote: Hello I use a charmm force field in gromacs. I almost finished my parametrization except for Lennard-Jones parameters. For this parameters I want to adopt the values in the charmm force field for the basic atom types. In gromacs I have to put this para

Re: [gmx-users] Umbrella_pull_simulation

I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes

[gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

Hello I use a charmm force field in gromacs. I almost finished my parametrization except for Lennard-Jones parameters. For this parameters I want to adopt the values in the charmm force field for the basic atom types. In gromacs I have to put this parameters in the ffnonbonded.itp file in the

Re: [gmx-users] Scaling/performance on Gromacs 4

Hi Sara, my guess is that 1500 steps are not at all sufficient for a benchmark on 64 cores. The dynamic load balancing will need more time to adapt the domain sizes for optimal balance. It is also important that you reset the timers when the load is balanced (to get clean performance numbers);

[gmx-users] Scaling/performance on Gromacs 4

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

Re: [gmx-users] Problem with simulation of Protein-DNA complex

Hi Tsjerk, I have checked and re-checked the structure and it seems fine. I also made sure to minimise the starting structure really well after pdb2gmx. Although it did not achive required precision, but machine precision instead. Also, the problem starts with the NVT, before that everything

Re: [gmx-users] problems with martinize.py

francesca vitalini wrote: Thanks Tsjerk, Florian, However I need the .gro file for the reverse transformation and I cannot simply obtain it through pdb2gmx as it won't recognize the atoms Use editconf to convert between .pdb and .gro (as well as other formats). pdb2gmx is for producing topo

Re: [gmx-users] problems with martinize.py

Thanks Tsjerk, Florian, However I need the .gro file for the reverse transformation and I cannot simply obtain it through pdb2gmx as it won't recognize the atoms Fatal error: Atom BB in residue ALA 1 was not found in rtp entry ALA with 8 atoms while sorting atoms. . Any help with that? Thanks a l

Re: [gmx-users] problems with martinize.py

On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote: > Just one last question Tsjerk, I was trying to load the cg.gro file > obtained with martinize in vmd and the program says it is unable to > load the molecule. the result of the martinize script looks like: > > MODEL1 > TITLE

Re: [gmx-users] problems with martinize.py

Hi Francesca, The output is written in .pdb format. That's also stated in the help. Cheers, Tsjerk On Mon, Feb 20, 2012 at 4:05 PM, francesca vitalini wrote: > Just  one last question Tsjerk, I was trying to load the cg.gro file > obtained with martinize in vmd and the program says it is unabl

[gmx-users] Re: gmx-users Digest, Vol 94, Issue 119

HI GROMACS users, Thank you mark for your advice.. As per these link http://en.wikipedia.org/wiki/Flying_ice_cube such as those using explicitly represented solvent under periodic boundary conditions - only the translational motion should be removed. Although it does not produce a pe

Re: [gmx-users] problems with martinize.py

Just one last question Tsjerk, I was trying to load the cg.gro file obtained with martinize in vmd and the program says it is unable to load the molecule. the result of the martinize script looks like: MODEL1 TITLE Protein in water CRYST1 29.094 29.094 29.094 90.00 90.00 90.0

Re: [gmx-users] Umbrella_pull_simulation

shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensib

Re: [gmx-users] problems with martinize.py

Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through

Re: [gmx-users] problems with martinize.py

Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by

Re: [gmx-users] Molecular Dynamics basics...

On 21/02/2012 12:11 AM, prashant kurkute wrote: Hi GROMACS users, I am a very novice to GROMACS.. .. My question may be very simple but very important to me..!!! These may be very basics... 1. What is the meaning of comm_mode and nstcomm.. I read the manual but

Re: [gmx-users] problems with martinize.py

Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition re

Re: [gmx-users] problems with martinize.py

Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining. Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini wrote: > I've changed that but it is s

[gmx-users] Molecular Dynamics basics...

Hi GROMACS users, I am a very novice to GROMACS.. .. My question may be very simple but very important to me..!!! These may be very basics... 1. What is the meaning of comm_mode and nstcomm.. I read the manual but unable to digest it..so please explain in mor

Re: [gmx-users] problems with martinize.py

I've changed that but it is still complaining... INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are o

Re: [gmx-users] problems with martinize.py

Hi Francesca, The problem is that the second line of your gro file indicates there are 2410 atoms in the file, while there are only 25. Did you manually remove water? In that case you have to update the number of atoms in the second line. The error message should be more explanatory though. Cheer

Re: [gmx-users] problems with martinize.py

I was using the one available from the tutorial but now I have downloaded the new one and it gives me still an error message like INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO

Re: [gmx-users] problems with martinize.py

Hi Francesca, Is this the latest version (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? If it is, please send me the input file and I'll fix the bug. Note that the previous version that was available online was one used in a workshop, while the script was still in beta.

Re: [gmx-users] water radial distribution function

On 20/02/2012 10:40 PM, Nidhi Katyal wrote: Dear all, I would like to plot g(OO) water radial distribution function.How should i use g_rdf or any other command to do this?Please help. Please read g_rdf -h, try things out and ask a focussed question. :-) Mark -- gmx-users mailing listgmx-u

[gmx-users] water radial distribution function

Dear all, I would like to plot g(OO) water radial distribution function.How should i use g_rdf or any other command to do this?Please help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

Re: Sv: Re: [gmx-users] double and single precision

On 20/02/2012 9:13 PM, Edvin Erdtman wrote: Hi again How do I "set the env.var. GMX_ENX_NO_FATAL"? I have tried in bash with: GMX_ENX_NO_FATAL=1 and then eneconv -e But I still get fatal error. http://en.wikipedia.org/wiki/Environment_variable#Getting_and_setting_environment_variables Mark

Re: Sv: Re: [gmx-users] double and single precision

Hi again How do I "set the env.var. GMX_ENX_NO_FATAL"? I have tried in bash with: GMX_ENX_NO_FATAL=1 and then eneconv -e But I still get fatal error. /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS >>> 2012-02-20 kl. 09:38, skrev Mark Abraham : > On 20/02/2012 7

[gmx-users] problems with martinize.py

Hi all, I'm trying to coarsegrain my structure using the script martinize.py and using my gro file as inmput and the dssp file with the second structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the pdb structure as input, I get the following error message that I really don't understand

[gmx-users] FW: Gromacs-GPU benchmark test killed after exhausting the memory

Sorry, I forgot to enclose the command line and output > mdrun-gpu -device > "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes" -deffnm md :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane

[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory

Hi, I have Gromacs- GPU version 4.5.5 and GTX 580. I run dhfr-solv-PME benchmark test (see below) and my run is killed after couple of hours when it exhausts all the computer memory, including the swap (2G + 4G swap). Has anyone encountered this problem? What do I do wrong? Thanks, Efrat -- gm

Re: Sv: Re: [gmx-users] double and single precision

On 20/02/2012 7:29 PM, Edvin Erdtman wrote: Hi So the best I can do now is to recreate the first part, and rerun "new" the simulations? If you have a full frame (positions+velocities+maybe energies, or a checkpoint file) then I expect so. Save your crossbreed files in case someone has a bet

Sv: Re: [gmx-users] double and single precision

Hi So the best I can do now is to recreate the first part, and rerun "new" the simulations? /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS >>> 2012-02-20 kl. 09:26, skrev Mark Abraham : > On 20/02/2012 7:19 PM, Edvin Erdtman wrote: > > Hi > > > > I have been runnin

Re: [gmx-users] double and single precision

On 20/02/2012 7:19 PM, Edvin Erdtman wrote: Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the doub

[gmx-users] double and single precision

Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic

[gmx-users] double and single precision

Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic