From: Yang MIngjun (
Date: Tue Sep 01 2009 - 09:03:13 CDT

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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