On 2/14/13 1:01 AM, Алексей Раевский wrote:
Hi, dear developers!
I want to ask you abou dynamics in implicit solvent. I have a complex of
animal protein - dimer/trimer. After modeling by homology I have built
another one from the plant organism. Dimer/trimer was constructed with
superposition method. The question is - can I use imlicit solvent model to
optimize and relax this complex? Is it real and where I can find suitable
parameters of mdp?
Infinite cutoffs with a nonperiodic unit cell are generally advisable for
running implicit solvent calculations. They don't parallelize well due to a bug
that I believe is still being fixed, so you can only run on 1-2 processors in
implicit solvent. Performance for large systems actually scales better in
explicit solvent, especially if you use GPU acceleration.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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