Re: [External] Boost value in aMD simulation

From: James Starlight (
Date: Wed Jul 23 2014 - 14:24:45 CDT

Dear NAMD users,
I'm very appologise, this question was adressed to both forums :-)
My question is refirement of loops predicted by modeller
the goal is
1- just refine loops but not refine rest of the protein (freezing it)
2- avoid to use the membrane, because I'd like to refine water expoised
regions of the membrane protein only
3- enhansing sampling engine to refine it quickly
4- do several refirement simulation, use PCA to test coverage (found shared
regions in PC projections of the loops conformations predicted by such
refirement from seveal simulations)

2014-07-23 23:14 GMT+04:00 Pino, James Christopher <>:

> Your greeting implies this went to the wrong forum.
> However, I am using aMD through amber also.
> I am curious what your goal is? Loop refinement of de novo models?
> James
> Vanderbilt University
> ________________________________________
> From: [] on behalf of
> James Starlight []
> Sent: Wednesday, July 23, 2014 6:30 AM
> To: Namd Mailing List
> Subject: [External] namd-l: Boost value in aMD simulation
> Dear Amber users!
> In this topic I would like to talk about information obtained from the
> amd.log concerning the reasonability of the values of boost potentials
> applied to my system. For my case I'm simulating protein in explicit water
> with the task to refine its loops appling position restraints on part of
> the protein (which I'd like to keep unchanged). Firstly I've performed cMD
> with no restraints to obtain all values needed to compute boost and alpha
> according to the impirical formuli presented in manual. Then I run 2 boost
> aMD with applied of the position restraints on the bigger part of the
> protein and see amd.log. According to themd.log the value of dihedral
> boost added to my system per step during amd simulation has been ~ 10
> Kcal/mol on each step. I wounder if the dihe boost of this value have been
> applied to the whole protein (including its restrained parts) or only to
> its unrestrained (in my case loops) parts? What the reasonable dUdihe
> should be expected in principle for the simulation of protein consisted of
> ~ 300 amino acids? I guess that this value should be nuch biger than
> several Kcal/ mol to obtain better sampling.
> Thanks for suggestions,
> James

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