Re: [External] Boost value in aMD simulation

From: Thomas Evangelidis (
Date: Wed Jul 23 2014 - 15:02:25 CDT

On 23 July 2014 22:24, James Starlight <> wrote:

> 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)
Do you realize how much time this protocol needs to reach convergence on
the eigenvectors of the accumulated trajectory (if that ever happens at
all)? Why not just create tens of thousands of loop models, cluster them
and start a simulation from the representative conformation of the
predominant cluster?

On another note, are these extracellular and intracellular loops so
important to invest that amount of labour on them? What kind of protein is
this? Can you upload some pictures on Dropbox to show us the protein with
the loops coloured differently?

> 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

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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