From: Yang MIngjun (
Date: Thu Sep 03 2009 - 01:37:21 CDT

Dear NAMD users,

   I still don't find an exact answer to my questions as follows and request your kindly help.
Many thanks.


>Dear NAMD users,
> We performed a MD simulation of a protein solvated in a truncated octahedron using >CHARMM (C31) software. The simulation was carried out under constant temperature and >pressure conditions with periodic boundary conditions. Now we are going to employ the >advantage of parallel run of NAMD to perform the same simulation again with different >initial velocities. Here are some questions I have after carefully reading the manual of >NAMD.

>1. If I use the same parameters for potential energy and boundary conditions as in CHARMM, can NAMD produce the same energy values of the system?
>2. For the truncated octahedron (TO), how to set the CellBasisVector1,2,3?
>In gromacs 3.2: (d, 0, 0) (1/3d, 2*sqrt[2]*d/3, 0), (-d/3, sqrt[2]*d/3, sqrt[6]*d/3)
>In CHARMM input file: set ax 87.35739
> set b 109.4712206344907
> crystal define octahedral @ax @ax @ax @b @b @b
> crystal build cutoff 60
>Someone posted in the mailing list that if the octahedron was built by tleap or xleap in >AMBER, the CellBasisVector1,2,3 should be set as:
> (d, 0, 0) (-1/3d, 2*sqrt[2]*d/3, 0), (-d/3, -sqrt[2]*d/3, -sqrt[6]*d/3)
>which is different from the ones in Gromacs3.2. But I don't know what causes the >difference. Is the orientation of the TO?

>How should I set the CellBasisVector1,2,3 with the TO I built, the orientation of which is different from the one built by tleap or xleap?

>3. Can NAMD read the .psf file successfully produced by CHARMM?
>Is there a convenient way to use the input files of CHARMM?

>I am new to the NAMD software. Any suggestion is greatly appreciated.

>Many thanks.


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