From: Namd Namd (namd_10_at_yahoo.com)
Date: Mon Jun 13 2011 - 14:29:40 CDT
Dear Namd experts,
I have to overcome some problems about force fields immediatelyto perform md via Namd. So I urgently need your help. Could you please help me out ?
By using CHARMM19 force field, I am trying to simulate the binary mixture consisting of A and B type molecules. I have some questions about topology and parameter files.
1. The first line of topology file
indicates CHARMM19 force field, as it is known.Is it possible to model the molecule A in the mixture with united atom model that treats –CHx groups as single interacting site and the molecule B with all atom model that treats each atom as a site?
2. In topology file, the line
atom N1 NYZ -.56
implies the atom with the name N1, the type NYZ, and a charge of -0.56. If NAMD automatically generates the angles and dihedrals according to the atom types defined in topology file, I think that the atom types have to be taken from CHARMM19 force field. But I am not sure that. Do the symbol for atom type (in my topology file NYZ) have to be one of the CHARMM19 atom types or is any other userdefined symbol (like NYZ) possible?
Thank you all for the responses.
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