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? 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 http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
