[gmx-users] Continuation of finished job

[Gia Maisuradze]

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?

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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>>
>>
>> -- 
>> ------------------------------------------------------
>> 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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