[gmx-users] All-bonds vs. H-bonds using CHARMM36

rajat desikan rajatdesikan at gmail.com
Thu Oct 31 19:21:15 CET 2013

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?

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?

P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on
lipidbook. Their .mdp constrains h-bonds

Thank you.

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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