From: Dimitar V Pachov (dpachov_at_brandeis.edu)
Date: Fri Aug 07 2009 - 19:50:30 CDT
I have prepared an Octahedral system in CHARMM (building, minimization, equilibration(in NPT)) and used the final coordinates as an input for testing runs in NAMD (2.6 and CVS version) that can after that be analyzed back with CHARMM. I defined CellBasisVectors in accordance with the CHARMM orientation of the OCTAhedral (i.e. the matrix of the vectors is symmetric). Then, I ran a short MD (100-200ps) and produced a DCD file with the "DCDUnitCell yes" option. The documentation claims this file is in CHARMM format and has to "contain unit cell information in the style of Charmm DCD files". However, when I read this NAMD produced trajectory file in CHARMM, it didn't seem to contain the correct "CHARMM style cell data". Why:
1) CHARMM + CORREL CELL module can extract cell data from trajectory files. I extracted the cell data (A,B,C, Alpha, Beta, Gamma + 6 lower diagonal values for the SHAPE symmetric matrix) from the CHARMM produced equilibration trajectory and compared it to the same data from the NAMD DCD file, and these data do not match. A,B,C values match (within fluctuation error), but while the CHARMM angles Alpha,Beta,Gamma are the correct 109.47* for OCTAhedral system, the NAMD trajectory gives values of 90.43* for all of the three angles. Also, the SHAPE matrices values are different.
2) Read the NAMD trajectory in CHARMM, build IMAGES within a certain cutoff based on the cell data for every frame in the DCD file, and save PDB files for the primary cell + the images. When looked in VMD, the images are very distorted and do not fill up the space around the primary cell (images attached).
Therefore, my questions are:
1. Does NAMD actually save the unit cell data in the DCD file in a CHARMM compatible format? If it does, why am I having problems? If it doesn't, what is the format then?
2. I tried to use the FixDCD utility to change the header of the NAMD DCD file (assuming it was in a "wrong" X-Plor format) and reuse it in CHARMM for analysis, but the obtained new trajectory file was reported not to "...CONTAIN CRYSTAL UNIT CELL DATA". I compared its header to a CHARMM produced trajectory containing crystal data, and although the two header structures looked similar, it seemed that some data were missing from the fixed DCD file. Why is that?
3. Or, am I missing something?
Thank you,
Dimitar
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