Re: Restart MD from a certain point?

From: Andreas Förster (docandreas_at_gmail.com)
Date: Thu Oct 14 2010 - 10:50:14 CDT

Dear Wendy,

I assume you created restart files, given that you're reading in
.restart.vel and .restart.xsc files. I found that having coordinates is
not enough. You need binary coordinates. Presumably VMD can create
them from your .dcd trace.

Use:
structure ionized.psf
coordinates step_700000.pdb <== placeholder
bincoordinates step_700000.coor <== binary coordinates
binvelocities DM_5ns.restart.vel
extendedSystem DM_5ns.restart.xsc

Hope that helps.

Andreas

On 14/10/2010 3:04, Axel Kohlmeyer wrote:
> dear wendy,
>
> 2010/10/14 Wendy González<locuswendy_at_gmail.com>:
>> Dear NAMD users:
>>
>> I have a MD simulation of 2040000 steps and I would like to restart it from
>> step 700000 applying some constraints. How can I do it?
>
> well, ideally by restarting from a restart. you did write out and saved
> periodic restarts like it is common good practice, or didn't you?
>
>> I tried to give as initial coordinate the step 700000 (see below) but it did
>> not work. Should I add other parameter?
>
> please explain _how_ it "did not work"?
>
> it is impossible to give advice without knowing what
> has happened and what you did exactly.
>
> cheers,
> axel.
>
>>
>> structure ionized.psf
>> coordinates step_700000.pdb
>> binvelocities DM_5ns.restart.vel
>> extendedSystem DM_5ns.restart.xsc
>>
>>
>
>
>

-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

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