[gmx-users] Storage of large output files

Dear All, We have started our venture into MD recently, for which we are using our in-house resources. Now that MD runs are giving very large output files like for trr files. The files keep piling up and using spaces on the work machines. This is creating problems with the depletion of space w

Re: [gmx-users] Constrains and TI

That sounds more reasonable...:) In fact I like the idea of using distance restraints, but I still doubt, that will work... I would really suggest to use the TI method. If you apply it properly it should give reasonable results. With proper application, speaking about using soft-core for VdW

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goetti

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Thank u very much for your suggestion, and now I had get the .gro file and .top file of ATP molecule, but how to I add the ATP molecule into the .gro and .top files of the protein? (If I paste the ATP's datas to the end of protein's file directly, and do genbox, then the result (.gro /.top file) on

Re: [gmx-users] publishing with development version of Gromacs

Hi, As long as you have the exact date you checked it out from CVS it is possible to obtain the same version again. However, bear in mind that CVS _does_ break periodically, and we don't check it like the released version. Before I do anything production-related with CVS I always check th

RE: [gmx-users] problems with parallel mdrun

Dear Mark, Thanks for the reply. I am using the following options for the electrostatics in the mdp file coulombtype = pme fourierspacing = 0.1 pmeorder= 4 optimize_fft= yes ewald_rtol = 1.0e-5 ewald_geometry = 3dc So if I understood you correc

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

As Mark suggested. If you have the parameters for your ATP, build an RTP-entry and afterwards, give the protein together with ATP into pdb2gmx... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettinge

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Yes, I found a server (ProDrg) can get the .gro and .top files of ATP molecule. --- Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Ins

Re: [gmx-users] problems with parallel mdrun

Mark Abraham wrote: > Gurpreet Singh wrote: >> I get the following errors while using paralled version of mdrun compiled >> with openmpi. >> mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1 >> * >> Program mdrun_d_mpi, VERSION 3.3.99_development_20070720 >> Source code file: gmx_parallel_3dfft.c

Re: [gmx-users] problems with parallel mdrun

singh wrote: Dear Mark, Thanks for the reply. I am using the following options for the electrostatics in the mdp file coulombtype = pme fourierspacing = 0.1 pmeorder= 4 optimize_fft= yes ewald_rtol = 1.0e-5 ewald_geometry = 3dc So if I under

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Be aware, that you can't use the ouput with every forcefield... Attaching the gro-file to your protein gro at the proper position (right after the protein) and building the correct topology should do the job. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical &

Re: [gmx-users] Storage of large output files

Monika Sharma wrote: Dear All, We have started our venture into MD recently, for which we are using our in-house resources. Now that MD runs are giving very large output files like for trr files. The files keep piling up and using spaces on the work machines. This is creating problems with the

Re: [gmx-users] Storage of large output files

Hi Monika, use trjconv -f your_trr_file_is_big.trr -o your_trr_file_is_compresses.xtc after your run. or change the frequencies for writing out coordinates, velocities etc in your mdp file like: nstvout = 1000; frequency to write velocities to output trajectory,

Re: [gmx-users] Storage of large output files

Thanks Mark for your reply. Thats a sound advice. I will really take care of. Actually, through my previous mail, I wanted to know that what other groups are using as storage devices for the backup of their large files, that must have figured out that which way is best-" economical and efficien

Re: [gmx-users] Storage of large output files

I've always used HDDs for the main backup/working copies, and DVDs for longer-term backup. You can get hold of 100x spindles of DVDs quite cheaply these days... I wouldn't call it convenient, though. - Original Message From: Monika Sharma <[EMAIL PROTECTED]> To: Discussion list for GR

Re: [gmx-users] Storage of large output files

This is an interesting topic and has been discussed before: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ We use a tape-drive for backups. /Erik 9 aug 2007 kl. 11.56 skrev Alan Dodd: I've always used HDDs for the main backup/working copies, and DVDs for longer-term backup.

RE: [gmx-users] problems with parallel mdrun

Dear Mark, As you suggested, i ran the simulations with fourier spacing of 0.08,0.09,0.10 & 0.11 with mpirun -np 4 mdrun_d_mpi -np 4 following is the output fourierspacing =0.08 --- Program mdrun_d_mpi, VERSION 3.3.99_development_20070720 Sourc

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Hi, If you are using any of the united atom GROMOS96 forcefields then there is already an rtp entry for ATP. Check out the .rtp files in the top folder. All you need to do is to have the ATP atoms in the pdb file the same as the atom names in the .rtp file for pdb2gmx to do all the work for yo

Re: [gmx-users] pressure scaling more than 1%

The system is a protein binding with one ligand and the ligand mutates to another one. The problem is found when lamda=1. First of all I run a energy minimization using an initial structure from the product of lamda=0.9. Then the problem happens when I run a equilibrium. Here is the mdp option: cpp

[gmx-users] Pull code with shuffle/sort options

Dear all, I have encountered noticeable differences while using the pull code with the -shuffle -sort options in parallel, as opposed to running in serial or in parallel without the options. Using -shuffle -sort, the dynamics of the molecule of interest appears to be unaffected by the pulling

[gmx-users] add to "doing simplest simulations

Sorry 'bout that, this time with the files... Gromacs Runs One Microsecond At Cannonball Speeds 2 1ETHET11 0.769 0.769 0.744 1ETHET22 0.769 0.769 0.794 1.53748 1.53748 1.53748 #include "ffgmx.itp" #include "OneEthane.itp" [ system ] ;Name pure etha

[gmx-users] doing simplest simulations

Hi, I'm doing a comparison in the aspect of speed between gromacs and an other MD-simulation-program, that isn't providing all the diffrent options of gromacs. My problem is, that the results I got from the simulations with gromacs aren't reasonable. E.g negative pressure and zero kelvin or ri

[gmx-users] Re: question about free energy. Gromacs user

Hi, > I have been reading your work about free energy calculations and it is > impressive. I want to estimate binding free energy for a ligand/receptor > complex and I would appreciate your valuable input on how to approach the > system I am using. It is the first time I attempt free energy > cal

Re: [gmx-users] problems with parallel mdrun

Carsten Kutzner wrote: Mark Abraham wrote: Gurpreet Singh wrote: I get the following errors while using paralled version of mdrun compiled with openmpi. mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1 * Program mdrun_d_mpi, VERSION 3.3.99_development_20070720 Source code file: gmx_parallel_

Re: [gmx-users] doing simplest simulations

Nicolas Schmidt wrote: Hi, I'm doing a comparison in the aspect of speed between gromacs and an other MD-simulation-program, that isn't providing all the diffrent options of gromacs. My problem is, that the results I got from the simulations with gromacs aren't reasonable. E.g negative pressu

Re: [gmx-users] Re: question about free energy. Gromacs user

> > Maybe it should be obvious, but (a) why are you constraining two > distances, and (b) are you sure your constraints aren't going to muck > with the internal degrees of freedom for the ligand? I would think one > would like to pull the ligand out of the receptor along some > particular directio

[gmx-users] Pull code with shuffle/sort options

I have encountered noticeable differences while using the pull code with the -shuffle -sort options in parallel, as opposed to running in serial or in parallel without the options. Using -shuffle -sort, the dynamics of the molecule of interest appears to be unaffected by the pulling potential.