[gmx-users] Continuation of finished job

[David]

On Thu, 2005-06-16 at 10:49 -0700, Gia Maisuradze wrote:
> Hi,
> 
> I have done 10ns MD simulation for one of the proteins. Now I want to 
> continue MD simulation of my finished job for another 10ns. I don't know how 
> I can do that. In order to run MD simulation first we should perform MD run 
> with position restraints and then perform full MD. In my case, when I want 
> to continue finished job what should I do?
> 
tpbconv -extend 10000

> Thanks in advance,
> 
> Gia
> 
> ----- Original Message ----- 
> From: "Gia Maisuradze" <gia at chem.unr.edu>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Wednesday, May 18, 2005 6:44 PM
> Subject: Re: [gmx-users] Root-mean-square deviation
> 
> 
> > Ran,
> >
> > Thanks. It works now.
> >
> > Gia
> >
> > ----- Original Message ----- 
> > From: "Ran Friedman" <ran at hemi.tau.ac.il>
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Sent: Wednesday, May 18, 2005 6:44 AM
> > Subject: Re: [gmx-users] Root-mean-square deviation
> >
> >
> >> Just use the -res flag.
> >>
> >> Ran.
> >>
> >> Gia Maisuradze wrote:
> >>
> >>> Hi,
> >>>
> >>> In my previouis email my question was about rmsd as a function of 
> >>> residue number. Later I found the same kind of question in archive, and 
> >>> the answer was g_rmsf program. I have tried this program and got rmsd as 
> >>> a function of atom number. I was trying to get an index file with all 
> >>> residues listed there, but g_rmsf still gives rmsd dependence on atom 
> >>> number. Perhaps I am not doing index file correctly. How can I create 
> >>> the index file with all residues listed? Could anyone help me with that?
> >>>
> >>> Thanks.
> >>>
> >>> Gia Maisuradze
> >>>
> >>>
> >>> ----- Original Message ----- From: "Gia Maisuradze" <gia at chem.unr.edu>
> >>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >>> Sent: Tuesday, May 17, 2005 10:27 AM
> >>> Subject: Re: [gmx-users] Root-mean-square deviation
> >>>
> >>>
> >>>> Hi,
> >>>>
> >>>> I am studying the dynamics of different mutants of lambda repressor. I 
> >>>> would like to calculate rmsd as a function of residue number. Gromacs 
> >>>> has a few different programs to calculate rmsd dependence on time, but 
> >>>> I could not find the dependence on residue number.
> >>>>
> >>>> Is there any program in Gromacs which can perform this kind of 
> >>>> calculation?
> >>>>
> >>>> Thanks.
> >>>>
> >>>> Gia Maisuradze
> >>>> _______________________________________________
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> >>>>
> >>>
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> >>> +++++++++++++++++++++++++++++++++++++++++++
> >>> This Mail Was Scanned By Mail-seCure System
> >>> at the Tel-Aviv University CC.
> >>
> >>
> >> -- 
> >> ------------------------------------------------------
> >> Ran Friedman
> >> Laser Laboratory for Fast Reactions in Biology
> >> Department of Biochemistry
> >> Faculty of Life Sciences
> >> Tel-Aviv University
> >> Tel. +972-3-6409824
> >> Fax. +972-3-6409875
> >> ------------------------------------------------------
> >>
> >>
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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