On 10/31/13 2:21 PM, rajat desikan wrote:
Hi,
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 the
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
http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp
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
--
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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