Hi Justin, In a recent post (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944) you commented that:
"Unless you can demonstrate that your changes in cutoffs do not produce artifacts or lead to other inaccuracies using robust test systems, I wouldn't recommend any deviations." I have the habit of reading the original forcefield papers and using their parameters directly. In this regard, I use rlist=rvdw=rcoulomb=0.8 nm for Amber03 (same parameters are used in the following tutorial: http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) ). My system is a protein in a water box with counter-ions and 0.1M NaCl. It is a NVT simulation at 310 K. My queries are the following 1) Are my parameters appropriate for Amber03? 2) How would I go about constructing robust test systems to demonstrate the validity of my parameters for a protein in a water box? What parameters do I measure? Energies? Any structural parameters in particular? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/rvdw-rlist-and-rcoulomb-for-Amber03-tp5010711.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
