Re: Restart MD from a certain point?

From: Wendy González (locuswendy_at_gmail.com)
Date: Thu Oct 21 2010 - 07:22:24 CDT

Thanks all of you, it worked now adding binary coordinates and I lookeed up
what is needed to enable constraints (I added two more atoms constrained).

2010/10/14 Andreas Förster <docandreas_at_gmail.com>

> 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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