Dear Justin, Thank you very much for your answer. I did not take this as a criticism of implicit solvent model. I was just wondering what was the origin of the limitations you were speaking of. I did some small implicit solvent simulations, but I must say that I have not thoroughly looked at the impact of cutoffs on energy conservation. I will be careful about that. About the bug for the implicit solvent code in GROMACS, is it only found in the new version 4.6 or it is also present in earlier versions such as in the 4.5 series? Thanks, Sebastien
> Date: Thu, 14 Feb 2013 10:48:51 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Implicit solvent > > > > On 2/14/13 10:21 AM, Sebastien Cote wrote: > > > > Dear Justin, > > 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". > > There is an existing limitation in Gromacs, related to constraints, that > causes > the implicit solvent code to fail when run on CPU if you try to use more than > 2 > processors. It is my understanding that someone (probably Berk) is working > on a > better fix than what is in place now. DD does not work with nonperiodic unit > cells and simple grid searches; you have to use particle decomposition. > Therein > lies another limitation. I have found that only infinite cutoffs (i.e. > rlist=rcoulomb=rvdw=0) lead to stable simulations, while any finite cutoff > (even > several nm in length) leads to poor energy conservation and unstable > trajectories. > > You can use GPU acceleration for implicit solvent simulations via OpenMM, but > support for this feature is minimal, at best, at the present time. > > Please do not take my comments as a criticism of implicit solvent methods; > they > are perfectly useful for a number of cases. > > -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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
