Re: [gmx-users] Reproducable MD runs on two PCs

I recompiled gromacs, lam, fftw3 on both PCs with the same version of intel compilers (before they were different, v. 10 & 12), set gen_vel=no and optimize_fft=no. With these changes I am getting agreement between two PCs within ~5% (was ~20% before). Ignore the nsteps value from the pasted mdp fi

Re: [gmx-users] Reproducable MD runs on two PCs

On 20/11/2011 7:31 PM, Igor Druz wrote: I recompiled gromacs, lam, fftw3 on both PCs with the same version of intel compilers (before they were different, v. 10 & 12), set gen_vel=no and optimize_fft=no. With these changes I am getting agreement between two PCs within ~5% (was ~20% before). Ign

[gmx-users] Problems with g_filter

Dear all I'm trying to use the follow command with a protein in DPPC and explicit water   g_filter -s md.tpr -f md.xtc -ol movie_filtered.pdb -fit -nf 5   Altough I selected protein group, the command export everything (water + protein + dppc).   How can I fix it?   Thanks in advance-- gmx-users

Re: [gmx-users] Reproducable MD runs on two PCs

If the -reprod option works fine and we can get complete reproducability on one machine, then I would think there must be a way of at least minimizing differences on two machines. I was hoping to pick on the experience with precision, whether it is worth having a go with a double precision compila

Re: [gmx-users] Reproducable MD runs on two PCs

On 20/11/2011 9:11 PM, Igor Druz wrote: If the -reprod option works fine and we can get complete reproducability on one machine, then I would think there must be a way of at least minimizing differences on two machines. Sure. Make as many things as similar as you can. Just don't bother trying

Re: [gmx-users] g_wham error

rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained suf

Re: [gmx-users] g_wham error

rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? >From literature, I kept it at 3000. Those

[gmx-users] query on partial charge entry in topology

Hi,   I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff directory), for each particle-type, there is a partial charge assigned to it. However, again in the .rtp file, for each residue, under each charge group, each of the atom is assigned  another partial charge assigned

Re: [gmx-users] query on partial charge entry in topology

Sanku M wrote: Hi, I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff directory), for each particle-type, there is a partial charge assigned to it. However, again in the .rtp file, for each residue, under each charge group, each of the atom is assigned another parti

Re: [gmx-users] GROMACS/ORCA QMMM

Dear Justin, The LJ and LJ.Excl files should be generated when you set bOpt = yes. What does the .inp file say. Is there !QMMMOpt or only !EnGrad? Christoph On 11/18/2011 06:20 PM, Jose Tusell wrote: Hi Justin, I tried using a larger step size but my system blew up... My guess is that I hav

[gmx-users] charmm 27 gromacs version mdp query

Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so

Re: [gmx-users] g_wham error

Justin, Should i turn off charges on the methane molecules? I have left them on. On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul wrote: > > > rajat desikan wrote: > >> My simulations are for 10 ns in each window. There is a lot of noise in >> my wham too. I am enclosing my wham for pullf (the

Re: [gmx-users] g_wham error

rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul

Re: [gmx-users] g_wham error

Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increa

Re: [gmx-users] g_wham error

rajat desikan wrote: Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple This is fundamentally incorrect. 53A6 is a united-atom force field, so each methane should be a single particle with 0 charge usi

Re: [gmx-users] g_wham error

rajat desikan wrote: Sorry, sorry...I have used Opls AA. The methane was going back and forth in the pulling during which I generated the configurations. Assuming you used a harmonic potential, that is to be expected. As long as you have set up reasonable spacing for your sampling windows

RE: [gmx-users] density

Last bit here, that is probably done using a RDF, which is a probability function, which you can then convert into a number of atoms in each shell. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Par

RE: [gmx-users] The time correlation functions for the orientation of the C-H

Check Chapter 8 and Appendix D of the manual. You can use g_analyze to generate an autocorrelation function for any data / property that you can feed it, if there isn't something built into a particular script. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of

RE: [gmx-users] NVT simulation

If you are just getting a feel for these things, use the -v switch with mdrun, this makes it verbose, and prints out lots of messages letting you know how much longer it will be etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Mon

[gmx-users] calculation equation of g_vanhove

Dear gmxers, I try to use g_vanhove in the gmx, but I do not find what it actually calculates because no equations are put in the manual. By the definition, it seems to be a bit different from those in some articles. Could you please give it clearly? Thanks a lot for any reply! Dr. Chaofu Wu

Re: [gmx-users] GROMACS/ORCA QMMM

I've tried the bOpt = true. Is the flag bOpt = yes? I'll try that and I'll let you know. Ramon On Sun, Nov 20, 2011 at 1:19 PM, Christoph Riplinger wrote: > Dear Justin, > > The LJ and LJ.Excl files should be generated when you set bOpt = yes. What > does the .inp file say. Is there !QMMMOpt o

Re: [gmx-users] GROMACS/ORCA QMMM

That solved it. In the ORCA manual for version 2.8 it says to use bOpt = true instead of bOpt = yes. And there is no mention of the mdp option in the gromacs manual or gromacs online mdp options. Ramon On Sun, Nov 20, 2011 at 4:57 PM, Jose Tusell wrote: > I've tried the bOpt = true.  Is the fl

[gmx-users] charmm 27 FF mdp query

Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so

[gmx-users] about temperature coupling

Dear gmxusers. I have problems about temperature coupling. Here is my parameter for temperature coupling. ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 298 I used "g_traj -f t

Re: [gmx-users] about temperature coupling

RuiTing Zhang wrote: Dear gmxusers. I have problems about temperature coupling. Here is my parameter for temperature coupling. ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t =

Re: [gmx-users] about temperature coupling

On 21/11/2011 2:12 PM, RuiTing Zhang wrote: Dear gmxusers. I have problems about temperature coupling. Here is my parameter for temperature coupling. ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 r

Re: [gmx-users] GROMACS/ORCA QMMM

When I run gromacs with bOpt yes I run into the a problem with the coordinates of my qm system: the initial coordinates are the following: NAME = ybu_em_qmmm.inp | 1> #input-file generated by gromacs | 2> !QMMMOpt TightSCF | 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym |

[gmx-users] Increasing time for simulation

Dear Justin, I am very sorry for a very basic question as i am beginner in Gromacs. Kindly do tell me that how can I increase time for the simulation. like 1st time i ran experiment on 1ns now i want to increase the time. kindly tell me that how can I do it and also tell that for a protein complex

Re: [gmx-users] GROMACS/ORCA QMMM

Jose Tusell wrote: When I run gromacs with bOpt yes I run into the a problem with the coordinates of my qm system: the initial coordinates are the following: NAME = ybu_em_qmmm.inp | 1> #input-file generated by gromacs | 2> !QMMMOpt TightSCF | 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS

Re: [gmx-users] GROMACS/ORCA QMMM

Yes. But where does the code go wrong? I'm reading the qm_orca.c file but I can't seem to know exactly were the factor of 10 is not accounted for. I see the factor of ten when going from gromacs to orca in (lines 219 to 221 of qm_orca.c file): qm->xQM[i][XX]/0.1, qm->xQM[i][YY]/0.1,

Re: [gmx-users] Increasing time for simulation

Saba Ferdous wrote: Dear Justin, I am very sorry for a very basic question as i am beginner in Gromacs. Kindly do tell me that how can I increase time for the simulation. like 1st time i ran experiment on 1ns now i want to increase the time. kindly tell me that how can I do it and also tell

Re: [gmx-users] about temperature coupling

Dear Justin and Mark： Thank you for your kind help！I think I figure out the problem Best Regards rtzhang -- 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/Search befo