[gmx-users] question about OPLS-AA force field -required bond constraints
Martin, Erik W
Erik.Martin at STJUDE.ORG
Thu Oct 10 18:17:00 CEST 2013
Hi, I'm new to both Gromacs and OPLS. I have always used CHARMM or AMBER before so am a bit confused about some idiosyncrasies.
When I go to a production run on my system (a protein in a truncated octahedron box of Tip4 water) I have removed all constraints. When I run grompp, I get an error telling me that a bond between a HG proton and OG oxygen of protein has an oscillation period of 9e-3 ps and is incompatible with my 1 fs time step. I am used to being able to run a completely unconstrained simulation with a 1 fs time step… so I'm assuming this is a property of OPLS-AA?
Could someone please let me know what the bond constraint requirements are for OPLS-AA and GROMOS forcefields (I'm going to need to use that next). I can't seem to find this information by searching but imagine its on a website somewhere?
Thanks a lot,
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