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

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue May 29 2018 - 12:53:52 CDT

Right! Thanks for pointing it out.

Giacomo

On Tue, May 29, 2018 at 1:37 PM, Brian Radak <brian.radak_at_gmail.com> wrote:

> +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/Resear
>>>> ch/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.
>>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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