From: Natalia Ostrowska (n.ostrowska_at_cent.uw.edu.pl)
Date: Tue Feb 22 2022 - 05:12:25 CST
Hi,
I tried nbtables, it is really well documented here:
http://www-s.ks.uiuc.edu/Research/namd/2.14/ug/node25.html just remember
not to mix up energy and force equations. There is also an extrabond
option, you can try this, but it might not work on large distances.
I made my pseudo bonds by adding artificial NBFIX entries between pairs of
atoms, you can see an example here
<https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0006349521005609*bib33__;Iw!!DZ3fjg!sf2JjvHow5671VFpldAyOjuS59R4TnWCWGUyOy1ERbVeIjLlstXLCPziZRChPLRPCw$ >,
in SI. It worked best for long bonds in my CG model, but implementing this
for a protein will be more problematic. You would have to change one of the
atom types to make sure the pair you are connecting have unique set of
types, otherwise some random part of the protein might be affected. This
will also require updating topology and parameter files, to include new
type with original parameters. You can try this if other methods don't fit
the case.
Regards,
Natalia Ostrowska
Univeristy of Warsaw, Poland
Centre of New Technologies
Biomolecular Machines Laboratory
wt., 22 lut 2022 o 05:45 Peter Freddolino <petefred_at_umich.edu> napisał(a):
> What is the form of the potential that you want to apply? The colvars
> module is almost certainly the right tool for what you want. See
> https://www.ks.uiuc.edu/Research/namd/2.12/ug/node53.html
> Best,
> Peter
>
> On Mon, Feb 21, 2022 at 3:09 PM Md Zobayer Hossain <mdzobaye_at_ualberta.ca>
> wrote:
>
>> Hi,
>> I am simulating a membrane protein complex. I need to put non bonded
>> extra potenial between two atoms of a proteins. I have seen the tabulated
>> energy table option for implementation. Did anyone use this option before.
>> Also is there any other way to put a potential between two atoms.
>>
>> Best regards
>> Zobayer
>>
>
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