[gmx-users] Re: LINCS with amber99SB ?
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 10 01:35:53 CEST 2011
Yun Shi wrote:
> Thank you for the reply. Just to clarify.
> In the original gromos 53a6 paper, all bonds were constrained, while in
> amber99sb paper only bonds involving H atoms were constrained. So as
> long as I stick to the same groups of bonds constrained as in the
> development of respective forcefields, it is always OK to use LINCS
> rather than SHAKE, right?
I've never had a problem with either approach.
> And for those bonds not constrained when using amber99sb force field,
> would GROMACS automatically apply the harmonic bond stretching
> functional form as specified in the [ bonds ] section of corresponding
> .itp files?
> Yun Shi wrote:
> > Hi all,
> > I want to do MD simulation with amber99SB force field, which I found
> > originally developed using SHAKE algorithm to constrain all bonds
> > involving hydrogen atoms. But it seems to me that SHAKE is still not
> > supported with domain decomposition in GROMACS4.5.4, and we can only use
> > LINCS for bond constraints if we want to run MD simulations in parallel.
> > So what should I use in simulating with amber99SB in parallel? LINCS
> > constraining allbonds? LINCS constraining hbonds only? Or just run with
> > SHAKE in one node?
> You should be able to use LINCS with either all-bonds or hbonds.
> Running your
> simulation in serial, even for a relatively small system, will likely be
> painfully slow.
> > I would be very grateful if someone could tell me the relative accuracy
> > (or if they are all good enough) and computational costs of these
> > options above.
> Either should be fine. LINCS is actually somewhat more stable than SHAKE.
> > And maybe I should ask this question in the developers mailing list, but
> > would GROMACS support SHAKE in parallel in the near future, like in a
> > 4.5.5 version?
> There will not be any new features in 4.5.5, and the 4.6 list of new
> features is
> already basically agreed upon. Gromacs is undergoing major code changes
> limit the amount of new features that will come out soon. You can file a
> feature request on redmine.gromacs.org <http://redmine.gromacs.org/>,
> but do not expect to see any activity on
> the issue until probably version 5.0.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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