[gmx-users] REMD

pawan raghav pwnrghv at gmail.com
Tue Jun 29 19:37:03 CEST 2010

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.

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.

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