[gmx-users] Understanding about the deleted trajectory file

Hi all, I want to know one thing that if delete .trr file, still job will be running (submitted job), where will go all these trajectories? Regarding .edr , .log the information will go to respective files by update. Can anyone tell that where trajectories will go, if those go som

[gmx-users] disulphide bonds

Dear Gromacs users, Is there any way to handle the disulphide bond formed between two independent fragments of a protein ? Precisely it is an inter disulphide bond between two fragments. If I keep the two fragments as separate objects while preparing the pdb file (using TER between the two fragmen

[gmx-users] user_defined_potential

Dear all, I have a question concerning the calculation of the Coulomb interaction energy with a user defined table. I generated a table where o n l y the coulomb interaction is multiplied by a factor a=2 and furthermore I used the following settings in the mdp file: energygrps= Protein

Re: [gmx-users] PCA uses average structure or reference structure

Hi Sunita, You should check the manual on this (and some statistics texts on PCA). g_covar calculates the average structure and takes the deviations around this average for further calculations. In that respect, you should be save. But the fact that you pose this question indicates that you may be

Re: [gmx-users] T-Coupling group

What's happening is that grompp is reaching the end of your topology (line 998) and identifying what it thinks is a problem. I'm guessing your peptide has 155 atoms? Using Protein Non-protein is fine, and is the best thing to do in this scenario. The warning is really meant to alert individu

[gmx-users] T-Coupling group

Hello everybody, I am trying to run a high temperature "rough" dynamic on a polypeptide to randomize its structure. When I pre-process the structure in the solvent I get the " T-Coupling group XXX has fewer than 10% of the atoms" error. This error is also described in the wiki and suggests to

Re: [gmx-users] Dealing with residues not in the topology database

Travis Craddock wrote: Hello, I am a new GROMACS user. My aim is to simulate the protein tubulin with a GTP molecule present. When attempting to create a topology file I receive a Fatal Error stating that the "Residue GTP is not found in the topology database". I understand that GTP is not

[gmx-users] Dealing with residues not in the topology database

Hello, I am a new GROMACS user. My aim is to simulate the protein tubulin with a GTP molecule present. When attempting to create a topology file I receive a Fatal Error stating that the "Residue GTP is not found in the topology database". I understand that GTP is not parameterized for the force

[gmx-users] PCA uses average structure or reference structure

hi all I did MD studies of a dimer using NAMD and charmm forcefields.now, in order analyze dynamic motions PCA was done using the command g_covar of GROMACS.here i gave .trr and .pdb as input.and selected backbone for analysis.the output obtained were average.pdb, average.trretc

FW: [gmx-users] Dynamical atom groups in 'index.ndx'

From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: RE: [gmx-users] Dynamical atom groups in 'index.ndx' Date: Wed, 25 Jun 2008 15:31:59 +0200 Hi, I think this would require complete rewriting of all the (required) analysis tools. Currently all tools assume that you have a static,

Re: [gmx-users] low cpu usage

It could be system-specific. Could you try out dppc in tutor/gmxbench or download gmxbench from gromacs' website (section Benchmark)? Regards, Yang Ye Dr. Bernd Rupp wrote: same problem as mpich2. regards, Bernd Am Mittwoch, 25. Juni 2008 schrieb Yang Ye: I don't think Python is to be bl

Re: [gmx-users] low cpu usage

> > > Am Samstag, 21. Juni 2008 schrieb ha salem: > > Dear users > > my gromacs is 3.3.3 my cpus are intel core2quad 2.4 Why don't you use Fedora's fftw & lam? I have been using Fedora's fftw & openmpi with Gromacs without any problems. Do you have some other processes running on you

Re: [gmx-users] low cpu usage

same problem as mpich2. regards, Bernd Am Mittwoch, 25. Juni 2008 schrieb Yang Ye: > I don't think Python is to be blamed. > How about lam-mpi? > > Regards, > Yang Ye > > Dr. Bernd Rupp wrote: > > Dear all, > > > > > > CPU: Intel(R) Core(TM)2 Extreme CPU Q6850 @ 3.00GHz > > System: fedora 8 > >

[gmx-users] Dynamical atom groups in 'index.ndx'

Dear Colleagues, Did not anybody try to implement a possibility to use a changeable 'index.ndx' when analyzing a trajectory (g_rdf, g_velacc, etc)? I mean that the atoms numbers in 'index.ndx' could change, being different for different frames. This trick can be used for evaluating properties of

Re: [gmx-users] low cpu usage

I don't think Python is to be blamed. How about lam-mpi? Regards, Yang Ye Dr. Bernd Rupp wrote: Dear all, CPU: Intel(R) Core(TM)2 Extreme CPU Q6850 @ 3.00GHz System: fedora 8 Kernel: 2.6.25.6-27.fc8 #1 SMP gromacs 3.3.3 correct compiled MPI : mpich or mpich2 We had the same problem with m

Re: [gmx-users] low cpu usage

Dear all, CPU: Intel(R) Core(TM)2 Extreme CPU Q6850 @ 3.00GHz System: fedora 8 Kernel: 2.6.25.6-27.fc8 #1 SMP gromacs 3.3.3 correct compiled MPI : mpich or mpich2 We had the same problem with mpich2. single processor run CPU load 100% double processor run CPU load around 70% quad processor run

Re: [gmx-users] (no subject)

Hello, Venkatesh Hariharan! To perform AFM pull you should provide an additional input file named xxx.ppa and append "-pi xxx.ppa" to mdrun arguments. You can read GROMACS online or paper manual for detail. 2008/6/24 VENKATESH HARIHARAN <[EMAIL PROTECTED]>: > Hello, > > I am new to GROMACS, an

[gmx-users] g_energy to compute free energy difference

Dear users, As the Gromacs manual mentioned, "g_energy" cauld calculate the free energy difference with an ideal gas state. After a simulation of protein in water with GMX3.3.1, I have tried the following commands to compute deltaG. 1. g_energy -f md.edr -fee -fetemp 300 -o energy1.xvg 2. g