From: Dimitar V Pachov (
Date: Thu Sep 03 2009 - 10:54:17 CDT

Dear Mingjun,

----- "Yang MIngjun" <> wrote:

| From: "Yang MIngjun" <>
| To: "Yang MIngjun" <>, "namd-l" <>
| Sent: Thursday, September 3, 2009 2:37:21 AM GMT -05:00 US/Canada Eastern
| Subject: Re: namd-l: CHARMM to NAMD
| Dear NAMD users,
| I still don't find an exact answer to my questions as follows and
| request your kindly help.
| Many thanks.
| Mingjun
| -----
| >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?

NAMD should produce compatible values, but not the same. Of course, it also depends on what you call "the same parameters".

| >
| >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

Isn't this cutoff value a bit high?

| >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?

The difference can be caused by two factors: 1) definition of the cell vectors and 2) their orientation wrt the coordinate system. GROMACS uses a different set of cell vectors for TO compared to CHARMM. The GROMACS cell vectors pass through the centers on hexagons that share a side with the same square face. CHARMM cell vectors pass through the centers of those hexagons that do not share a side with the same square. Obviously, the CHARMM's definition of the cell vectors comes from the symmetry requirement to end up with a symmetric shape matrix (this matrix contains the components of the cell vectors wrt to the coordinate system).

| >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?

You can set up your cell vectors in a number of different ways each of them producing a different from the AMBER's orientation. It is easy to get an orientation different from another; what might be hard is to get an orientation can coincides with another. You need a CHARMM compatible orientation, so you basically have to find what orientation the TO should have wrt to the origin so the components of the CHARMM defined cell vectors form a symmetric matrix.

| >3. Can NAMD read the .psf file successfully produced by CHARMM?

Yes, if you save it in a XPLOR format.

| >Is there a convenient way to use the input files of CHARMM?

No, unless you find a correspondence between the NAMD keywords and the CHARMM keywords such that the defined values are transferable.

| >I am new to the NAMD software. Any suggestion is greatly
| appreciated.
| >Many thanks.
| Best.
| Mingjun
| -----

Dimitar V Pachov
PhD Candidate
Physics & Biochemistry Department     Phone: (781) 736-2326
Brandeis University, MS 057           Email:

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