Re: Re: vmd-l: Large number of harmonic distance restraints

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue May 29 2018 - 11:36:46 CDT

Hi nick,

depending on your needs (if the restraints are only between atoms atoms and
the atoms are not too far apart), the most efficient way might be the
extraBonds
<http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html#SECTION00086400000000000000>feature,
which can be parallelized.

Best,
Ajasja

On Tue, 29 May 2018 at 18:27, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> hello nick,
>
> this is a question for the NAMD list not the VMD list. so i am copying
> namd-l instead of vmd-l
>
> ​what you describe sounds like something that you might want to implement
> using TclForces.
> it also might be possible with colvars.
> mind you, ​in both cases, your restraint forces will have to be computed
> on the global state, and thus cannot be parallelized and thus will impact
> parallel efficiency.
>
> axel.
>
>
> On Tue, May 29, 2018 at 12:04 PM, Nick Palmer <tuf90798_at_temple.edu> wrote:
>
>> Hello everyone,
>>
>> I would like to set up a simulation with a large number of different
>> distance restraints between atoms. I was wondering how I would be able to
>> do this.
>>
>> I have looked at colvars, and it seems to do what I want, however all the
>> information I can find on it shows distance restraints only between two
>> groups, and I would like to do maybe around 100 groups. I have also seen a
>> similar question here (
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2006-2007/2185.html
>> )
>> on the mailing list and it was saying to use the freeEnergy calculation's
>> urestraint command, however I just learned that these methods have been
>> depreciated.
>>
>> So is there a way to have a large amount of constraints in one colvars
>> method?
>>
>> Thank you in advance!
>>
>> --
>> Nicholas J. Palmer
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>

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