[gmx-users] How to get topol.top files from DRGGMX.ITP files?

Dear all, Am using Dundee prodrug server for the simulation of polymers..I have generated DRGGMX.ITP files for running gromacs simulation.How to get a topology file with .top extension so that i can use it in the grompp step from this. I used x2top command to generate topolgy file with DRGFIN.GR

Re: [gmx-users] How to get topol.top files from DRGGMX.ITP files?

varsha gautham wrote: Dear all, Am using Dundee prodrug server for the simulation of polymers..I have generated DRGGMX.ITP files for running gromacs simulation.How to get a topology file with .top extension so that i can use it in the grompp step from this. I used x2top command to generat

[gmx-users] query about random velocity generation

Dear Sir,   I want to simulate the same system at different temperatures using different velocities & want to investigate whether the simulations converged or not.. For that should we alter the default  gen_seed value, if yes, then can  we choose the gen_seed value arbitrary or  is there any ran

[gmx-users] restarting a replica exchange simulations

 Hi, I had previously ran a replica exchange molecular dynamics simulation for 10ns. There were 17 ".tpr" input files for 17 replicas at 17 different temperatures. However, the run had stopped and now I need to restart it. I had generated 17 ".tpr" files for the rest of the s

Re: [gmx-users] query about random velocity generation

Hi Sangeeta, Different temperatures always come with different velocities, as these are related to each other. If you want to have different simulations for the same temperature then you have to change the number for gen_seed. As for the range, you're stuck with that for a signed (?) int, but that

Re: [gmx-users] query about random velocity generation

Hi Sangeeta I don't know if it's the best option, but in a situation like yours I just used gen_seed = -1 (minus 1). By this way every time you do a simulation the gen_seed number will be different, because the program generates a random number. I hope this will help. Nuno Azoia Tsjerk Was

Re: [gmx-users] restarting a replica exchange simulations

sarbani chattopadhyay wrote: Hi, I had previously ran a replica exchange molecular dynamics simulation for 10ns. There were 17 ".tpr" input files for 17 replicas at 17 different temperatures. However, the run had stopped and now I need to restart it. I had generated 17 ".tpr"

RE: [gmx-users] restarting a replica exchange simulations

> Date: Sat, 31 Jan 2009 01:30:11 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] restarting a replica exchange simulations > > sarbani chattopadhyay wrote: > > Hi, > > I had previously ran a replica exchange molecular dynamics > > simulation

[gmx-users] Re: Gromacs 4 bug?

If someone is interested: Finally our nodes are working fine using Fedora Core 8, fftw-3.1.3, openmpi-1.3 and gromacs-4.0.3. Thank you very much for your time and effort! cheers Bernhard Message: 2 Date: Thu, 15 Jan 2009 08:37:16 +0100 From: patrick fuchs Subject: Re: Subject: Re: Re: [gmx

[gmx-users] IN4 molecule type error

Dear Gromacs users, I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial for a test run and i have ended up with following error. Please try to help me creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90# checking input for internal c

Re: [gmx-users] IN4 molecule type error

Ms. Aswathy S wrote: Dear Gromacs users, I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial for a test run and i have ended up with following error. Please try to help me creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90# chec

[gmx-users] gromacs 3.3.3 vs 4.0.3 performance

Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 (30% higher hours/ns), for few systems (512 molecules of 5-15 sites, nstlist=10) I tried. This

Re: [gmx-users] gromacs 3.3.3 vs 4.0.3 performance

Dimitris Dellis wrote: Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 (30% higher hours/ns), for few systems (512 molecules of 5-15 sites,

Re: [gmx-users] gromacs 3.3.3 vs 4.0.3 performance

Justin A. Lemkul wrote: Dimitris Dellis wrote: Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 (30% higher hours/ns), for few systems (512

RE: [gmx-users] "nstlist=-1" dosen't work for parallel runs

He Berk, I've sent it to the bugzilla. Could you have a look? Thanks very much! Lanyuan From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] "nstlist=-1" dosen't work for parallel runs Date: Thu, 29 Jan 2009 23:32:43 +0100 Hi, I just tested it and it runs fine for me

Re: [gmx-users] gromacs 3.3.3 vs 4.0.3 performance

Dimitris Dellis wrote: Justin A. Lemkul wrote: Dimitris Dellis wrote: Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 (30% higher hours/ns

Re: [gmx-users] gromacs 3.3.3 vs 4.0.3 performance

David van der Spoel wrote: Dimitris Dellis wrote: Justin A. Lemkul wrote: Dimitris Dellis wrote: Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower than

SV: [gmx-users] Grompp error in 4.x regarding dihedral multiplicity

Hi again, Thank you very much for your reply Mark. Now, I have a dihedral with the following form: 22232425 1 0.0 7.471 22232425 1 0.0 3.9 2 22232425 1 180.0 1.1 3 22232425 1

[gmx-users] energy groups

Hi, I tried to make energy groups based on chain id and atom type. My purpose is to select atoms in chain A and B without Hydrogen atoms . This is the command: make_ndx -f a.pdb -o a.ndx < make_ndx.input >a.log cat make_ndx.input del 1-9 chain A and B& !a H* chain C& !a H* q And then run gr

Re: [gmx-users] energy groups

Liu Shiyong wrote: --- Program grompp, VERSION 4.0.2 Source code file: grompp.c, line: 150 Fatal error: atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in different energy groups ---

[gmx-users] Melittin in methanol...

Dear Justin, Even with the new force field I am getting the same result. My methanol. gro file , em.mdp, pr,mdp and md.mdp files looks like these Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001 648 1MeOH Me11 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643 1MeOHO2

Re: [gmx-users] Melittin in methanol...

sharada wrote: rlist = 0.5 rcoulomb= 1.4 rvdw= 0.8 You are using cut-off electrostatics by default, so you are probably getting some bad artifacts (use PME instead). Also, the values of rlist, rcoulomb, and rvdw you are using do not correspond

[gmx-users] Melittin in methanol...

Dear Justin, Even with the new force field I am getting the same result. The methanol. gro file , em.mdp, pr,mdp and md.mdp files looks like these Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001 648 1MeOH Me1 1 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643 1MeOH O2 2 1.978 1.415 1.082 0

Re: SV: [gmx-users] Grompp error in 4.x regarding dihedral multiplicity

Sarah Witzke wrote: Hi again, Thank you very much for your reply Mark. Now, I have a dihedral with the following form: 22232425 1 0.0 7.471 22232425 1 0.0 3.9 2 22232425 1 180.0 1.1 3 222

[gmx-users] "No default proper Dih.type

Dear all, Am trying to do simulation of DPPC membrane.Am using ffgmx force field,because other force fields doesnt have DPP residue,so got an error saying "Residue DPP not in topology database. So i generated topology file using pdb2gmx -ff gmx -f inp.pdb -o out.gro now after few more steps i up