[gmx-users] implicit solvent with periodic molecules
jalemkul at vt.edu
Tue Nov 3 12:12:56 CET 2015
On 11/3/15 3:36 AM, Анна Павловна Толстова wrote:
> Hello again!
> My problem with implicit solvent is still unsolved. In gromacs manual and
> in gmx-users mail list was also mentioned that for implicit salvation all
> cut-offs should be switched to zeros. In that case PBC don't work. I've
> tried to perform simulation with implicit solvent and usual cut-offs of 1,4
> nm, but protein tertiary structure eventually after 1 ns started to
> collapse: different alpha-chains twisted around each other moved from each
> other. It seems like protein gained denaturation after. But it was ok with
> explicit solvent along 150 ns simulation.
> So that is the question:
> If it is possible to use PBC and periodic molecules with implicit solvent,
> what value for cut-offs should I take? My system is a big protein of 340
> kDa and a graphite sheet.
Long cutoffs (e.g. 4.0 nm) are common with implicit models. If you've already
got 150 ns of explicit solvent simulation, what's the point of the implicit? I
don't see much benefit of doing implicit anyway; questionable physical model, ad
hoc changes to cutoffs required to enforce stability, poor parallel scaling. I
think explicit is much more valid.
> Thanks in advance for answers.
> С уважением,
> Толстова Анна
> 2015-10-29 14:48 GMT+03:00 Vitaly V. Chaban <vvchaban at gmail.com>:
>> Yes. It is formally possible.
>> I do not think that implicit solvation precludes PBC usage.
>> On Thu, Oct 29, 2015 at 9:40 AM, Анна Павловна Толстова <
>> tolstova at physics.msu.ru> wrote:
>>> Hello, gmx_users.
>>> Is that possible to simulate a protein adsorption on graphite sheet with
>>> implicit solvent? It works good in vacuo and with explicit solvent with
>>> periodic-molecules = yes. But implicit solvent requires no PBC so that
>>> periodic molecules should be switched off too. Is there any idea how to
>>> perform this simulation?
>>> Best wishes,
>>> Tolstova Ann
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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