[gmx-users] Implicit solvent
sebastien.cote.4 at umontreal.ca
Thu Feb 14 16:21:38 CET 2013
I am not sure to follow you. You essentially say that it is better to avoid using implicit solvent i.e. the generalized Born-formalism implemented in GROMACS?
For the case of optimizing and relaxing a system (expecting short MD), I agree that it might be preferable to use explicit solvent.
But for some systems, such as the oligomerization of a protein from a random state, explicit solvent can make this problem intractable in MD (inefficient sampling of conformational space due to too many degrees of freedom from the solvent) or REMD (too many processors to use due to too many degrees of freedom).
I saw some tutorials and workshops suggesting larger cutoffs when using implicit solvent as the non-bonded function do tend to zero at long range. Then, domain decomposition can be used over particle decomposition.
Could you clarify your point please? Especially, your statement saying that : "you can only run on 1-2 processors in implicit solvent".
> Date: Thu, 14 Feb 2013 08:03:28 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Implicit solvent
> 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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