Re: [gmx-users] Forces in source code

Thank You! I'll try to get what you writed, so, perhaps, I'll write about my success or its lack! 12 декабря 2010 г. 4:42 пользователь Mark Abraham написал: > > > On 12/12/10, Петр Попов wrote: > > Hello, dear gmx-users. > > I want to decompose PMF, but I c

Re: [gmx-users] Forces in source code

To protein-protein and protein-lipid components, for example. 2010/12/12 David van der Spoel : > On 2010-12-11 22.52, Петр Попов wrote: >> >> Hello, dear gmx-users. >> >> I want to decompose PMF, but I can't use -rerun option for this > > decompose into wh

[gmx-users] Forces in source code

Hello, dear gmx-users. I want to decompose PMF, but I can't use -rerun option for this because I get this PMF due to pull force. And also .trr files are large to do md with different energy groups to get PMF. So, I need to adopt source code for this task. Could you help me and give me any advices?

Re: [gmx-users] output force - 2

Is it possible to slightly change the source code to adjust output of pullf in appropriate form? And if it is, how? Petr. 12 октября 2010 г. 17:49 пользователь Justin A. Lemkul написал: > > > Петр Попов wrote: >> >> Is the way to decompose pull force? >> > >

Re: [gmx-users] output force - 2

Is the way to decompose pull force? 2010/10/12 Justin A. Lemkul > > > Петр Попов wrote: > >> Hello dear gmx-users! >> >> So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc. >> then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top

[gmx-users] output force - 2

Hello dear gmx-users! So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc. then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL (in md.mdp: energygrps = System) after that I did: mdrun_d -s

Re: [gmx-users] output force

= Y Y Y > pull_constr_tol = 1e-6 > pull_nstfout= 1 > pull_nstxout= 1 > pull_ngroups= 1 > pull_group0 = a > pull_group1 = b > pull_init1 = 0.700 > pull_start = no > pull_k1 = 1000 > lincs_iter

Re: [gmx-users] output force

And what if I have four helices in Protein and a,b,c,d group for each helix in index.file and I want to get a-c pmf? 10 октября 2010 г. 21:20 пользователь Justin A. Lemkul написал: > > > Justin A. Lemkul wrote: > >> >> >> Петр Попов wrote: >> >>> Unf

Re: [gmx-users] output force

= 2 energygrps = Protein Protein I just replace in .mdp file line energygrps = System and the error is: Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 2) What should I do to avoid this? 10 октября 2010 г. 20:01 пользователь Петр Попов написал: > Thank you very much! > &

Re: [gmx-users] output force

Thank you very much! 10 октября 2010 г. 19:58 пользователь Justin A. Lemkul написал: > > > Петр Попов wrote: > >> So if I want to get protein-solvent component I should add in .mdp: >> >> energygrps = Protein SOL >> >> ? >> >> > Yes, and s

Re: [gmx-users] output force

So if I want to get protein-solvent component I should add in .mdp: energygrps = Protein SOL ? 10 октября 2010 г. 16:41 пользователь Justin A. Lemkul написал: > > > Петр Попов wrote: > >> Thank you for response! >> One more question: >> How can I get file wi

Re: [gmx-users] output force

run -rerun, but > not mid-simulation. > Mark > > - Original Message ----- > From: Петр Попов > Date: Saturday, October 9, 2010 21:41 > Subject: [gmx-users] output force > To: gmx-users@gromacs.org > > > Hello dear gmx-users! > > > > When calculated f

[gmx-users] output force

Hello dear gmx-users! When calculated forces in gromacs to produce pmf, we have the net force in output. For example: ... # # Giving Russians Opium May Alter Current Situation # @title "Pull force" @xaxis label "Time (ps)" @yaxis label "Force (kJ/mol/nm)" @TYPE xy 0.00

Re: [gmx-users] Split pmf

2010/10/4 Jochen Hub > On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote: > >> Hello, dears gmx-users! >> >> I posted a message, but didn't get a response, it was my first one, so may >> be I did something wrong. Anyway, here it is: >> >> I've alr

[gmx-users] Split pmf

Hello, dears gmx-users! I posted a message, but didn't get a response, it was my first one, so may be I did something wrong. Anyway, here it is: I've already run md and got pmf and it's correct. But I want to get not just a pmf of total force, but several profiles each of which corresponds to th

Re: Re: [gmx-users] Free Energy Calculation

>> Hello, dear users! >> >> I want to study different components in total free energy. >> Could you tell me in what gromacs program and in what place exactly force and energy are calculated? >I think your question is too general. I don't know whether you've already done a calculation, are planning

[gmx-users] Free Energy Calculation

Hello, dear users! I want to study different components in total free energy. Could you tell me in what gromacs program and in what place exactly force and energy are calculated? With best regards! Popov Petr -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis