[gmx-users] All-bonds vs. H-bonds using CHARMM36
rajatdesikan at gmail.com
Thu Oct 31 21:43:11 CET 2013
Thank you, Justin!
I did intend to use h-bonds for the CHARMM36 simulations and all-bonds
elsewhere (depending on the FF). I just wanted some clarity before I
On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/31/13 2:21 PM, rajat desikan wrote:
>> In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds
>> are constrained for the lipid simulations using SHAKE (excerpt from the
>> paper below)
>> "Consistent for all of these simulations was the use of a 1 fs time step
>> and constraining of the hydrogen atoms using the SHAKE algorithm."
>> For a membrane-protein system, is constraining all-bonds via LINCS the
>> right option while using CHARMM36?
> Normally, as the paper states, only bonds involving H are constrained with
> CHARMM. LINCS is a suitable replacement for SHAKE, though you can use
> SHAKE in Gromacs if you want. LINCS is generally more robust.
> There was a mention somewhere (I forgot) that constraining all-bonds
>> probably prevents alkane isomerisations in membranes, which could lower
>> melting temperature. I intend to simulate a POPC bilayer. Can someone with
>> experience please shed some light on this?
> Can't comment on this, but I doubt there is any issue if you don't
> constrain all bonds.
> P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on
>> lipidbook. Their .mdp constrains h-bonds
> It is very uncommon that such input files exist without specifically
> requesting them; if this is exactly what the authors used, I see no reason
> to deviate from it unless you have a demonstrably superior protocol.
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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