Re: Issue with rhombic dodecahedron / CHARMM compatibility

From: Dan Bolintineanu (
Date: Mon Dec 04 2006 - 17:12:58 CST

 I'm trying to run some solvated MD simulations using a rhombic
 dodecahedron (RHDO) box shape. I want to do the model building in
 CHARMM, then use NAMD for the production runs, then use CHARMM for
 analysis. NAMD claims to be fully compatible with the CHARMM
 trajectory format, but as it turns out, this doesn't seem to hold for
 RHDO simulations. After successfully building and minimizing the model
 in CHARMM, I try to load it into NAMD (after using the crd2pdb
 conversion utility).
 In NAMD, the van der Waals energy is through the roof, due to bad
 image contacts - I know this because using a much larger box
 definition in NAMD results in a reasonable energy.
 I tried COOR CONV ALIGNed SYMMetric before exporting the CHARMM crd
 file, but no avail.
 If I then re-build the model in NAMD, and produce a trajectory, I
 cannot read it in CHARMM and perform any image operations. I know
 there is a compatibility issue with the way unit cell angles (alpha,
 beta, gamma) are stored, but I think there is also a compatibility
 issue with the orientations of the unit cell.

 I got the CellBasisVectors corresponding to the RHDO shape from the
 GROMACS manual, which lists two orientations for the RHDO shape: one
 which has a square cross-section with the XY plane, the other with a
 hexagonal cross-section. I've tried every combination of COOR CONV
 ALIGN/SYMM and the two different cell basis vector configurations. I
 know that the cell basis configurations DO represent an RHDO, since
 extensive minimization and dynamics in NAMD does result in an
 RHDO-shaped water box (when viewed in VMD).

 Furthermore, I have tried several of the available TCL scripts to
 unwrap a NAMD trajectory produced with the above setup, and they all
 yield ridiculous output. Has anybody been able to successfully port
 RHDO-based simulations between charmm and NAMD, or at least
 wrap/unwrap an RHDO simulation produced by NAMD?

 Any advice on this would me much appreciated.

 Dan Bolintineanu

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