[gmx-users] implicit solvent with periodic molecules
Анна Павловна Толстова
tolstova at physics.msu.ru
Tue Nov 3 09:36:16 CET 2015
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.
Thanks in advance for answers.
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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