From: Dimitar V Pachov (dpachov_at_brandeis.edu)
Date: Thu Sep 03 2009  10:54:17 CDT
Dear Mingjun,
 "Yang MIngjun" <yangzch_at_mail.ustc.edu.cn> wrote:
 From: "Yang MIngjun" <yangzch_at_mail.ustc.edu.cn>
 To: "Yang MIngjun" <yangzch_at_mail.ustc.edu.cn>, "namdl" <namdl_at_ks.uiuc.edu>
 Sent: Thursday, September 3, 2009 2:37:21 AM GMT 05:00 US/Canada Eastern
 Subject: Re: namdl: 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
 
 DICP,CAS

 >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
 
 DICP, CAS
 ======================================================== Dimitar V Pachov PhD Candidate Physics & Biochemistry Department Phone: (781) 7362326 Brandeis University, MS 057 Email: dpachov_at_brandeis.edu ========================================================
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