[gmx-users] REMD

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 29 19:43:00 CEST 2010

pawan raghav wrote:
> Dear Justin,
> No dear I have not modelled the membrane, my protein is a simple protein 
> which contained a loop about 59 amino acids. So I am intrested to model 
> this loop through MD simulation. In this concerned I did 15 ns 
> simulations, but right now don't know how to perform sampling for my 
> protein (which is not a membrane, thermophilic or mesophilic protein) on 
> same temperature i.e. 300k. In this regard is it correct to perform 
> REMD, if yes then tell me how to perform it on single CPU? I am asking 
> from you again to sure I can perform ot is it right to use REMD in my 
> protein condition which in not a thermophilic protein. I think that REMD 
> can only apply to those proteins which are thermophilic or mesophilic. 
> please comment on this.

REMD has nothing to do with whether or not the protein is thermophilic.  Please 
do some background reading on the technique.  You need multiple processors to 
run the simulation.  The different replicates must be run concurrently so that 
they may periodically exchange.

Since you are not modeling a membrane, I again wonder how you settled on the 
force field you did.  Not that I think there's anything wrong with 53A6 (except 
for a bias towards extended structures, which you would have discovered with a 
bit of background reading).  Just be prepared to justify your choice to a 
critical audience...

> Yes I wanted to sample loop dynamics, for which you have mentioned 
> to run several simulations at the relevant (physiological?) temperature. 
> Is it mean to run several (2,3,4..etc) diferent simulations at different 
> time steps like 10ns, 15ns, 20ns, 30 ns etc. and analyze those results 
> to obtain some averages from each and every simulations but it gives 
> several averages values then how to sample all these simulations and 
> finally how to get the average from these simulations.

My suggestion was to run several simulations of equivalent length (such that the 
properties of interest converge) and obtain averages not only along each 
simulation, but also among all of them.


> -- 
> Pawan


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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