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

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue May 29 2018 - 12:37:00 CDT

+1

extraBonds is almost certainly the easiest and most performance effective
way to add forces between atoms. It also scales essentially perfectly with
normal MD, while colvars and TclForces will not in many cases.

Cheers,
BKR

On Tue, May 29, 2018 at 12:36 PM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com
> wrote:

> 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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