[AMBER] PMEMD conditions for solvent bulk characterization?

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Mon, 17 Oct 2011 17:05:31 -0500

Dear Amber users,

I am simulating some organic solvents using PME MD in with Langevin
thermostat.

Are there any flags I need to watch out for while determining bulk
properties, like density, Diffusion coefficient, etc?

For example, shouldn't nscm be set to zero for diffusion data?

Any other caveats that I should know about?

A relatively recent article,

dx.doi.org/10.1021/ct2002122 | J. Chem. Theory Comput. 2011, 7, 2240­2252


looked at benzene with several ff's and had constrained ALL bonds with
LINCs in gromacs even though the time step was 1 fsec.

I could see constraining the hydrogens, but why the carbons also?

Thanks very much for your help in advance!

Dean 
-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 17 2011 - 15:30:02 PDT
Custom Search