[gmx-users] Implicit solvent

Justin Lemkul jalemkul at vt.edu
Thu Feb 14 14:03:28 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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