[gmx-users] MD run with position restraints

[Gia Maisuradze]

David,

Thanks.

Gia

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, September 23, 2005 10:16 AM
Subject: Re: [gmx-users] MD run with position restraints


> On Fri, 2005-09-23 at 10:10 -0700, Gia Maisuradze wrote:
>> Thanks for the web-site, there are a lot of interesting stuff there.
>> However, I could not find the answer on my question. MD run with position
>> restraints should be shorter than full run, but it is not clear for me 
>> how
>> short. I am going to run long 100ns MD simulation. How long should I run 
>> MD
>> with position restraints?
> It's up to you to decide. A couple of 10s of ps usually is sufficient.
> Check energy and density convergence.
>>
>> Thanks in advance,
>>
>> Gia
>>
>> ----- Original Message ----- 
>> From: <leafyoung81-group at yahoo.com>
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Sent: Thursday, September 22, 2005 6:24 PM
>> Subject: Re: [gmx-users] MD run with position restraints
>>
>>
>> --- Gia Maisuradze <gia at chem.unr.edu> wrote:
>>
>> > Hi,
>> >
>> > I am going to run long MD simulation (100ns).
>> > According to manuel first I
>> > should run MD with position restraints and then full
>> > MD run without
>> > restraints. I was wondering how many nanosecond MD
>> > run with restraints I
>> > should perform in my case.
>> http://indigo1.biop.ox.ac.uk/MD_workshops/equilibrium.pdf
>> >
>> > Thanks in advance,
>> >
>> > Gia Maisuradze
>> >
>> >
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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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