[gmx-users] Continuation of finished job

[Gia Maisuradze]

David,

Thanks for your reply. I have used tpbconv for creation of run input file 
.tpr. So now I just need to run full MD simulation (no MD run with position 
restraints). Am I correct?

Thanks again,

Gia

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, June 16, 2005 11:31 AM
Subject: Re: [gmx-users] Continuation of finished job


> 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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> -- 
> 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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