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#12612 - 12/04/06 02:03 AM coor conv, RHDO and NAMD
Dan_B Offline
Forum Member

Registered: 05/23/06
Posts: 35
Loc: Minneapolis, US
This question is only half-CHARMM related, but I thought I'd give it a shot anyway:

I'm trying to run some solvated MD simulations using an RHDO crystal 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.
Now, NAMD uses a more general form in defining the crystal unit, involving something called cell basis vectors. These in turn I got 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).
The RHDO thus visualized looks to be at a different orientation than that produced by CHARMM, either with the SYMM or ALIGNed convention.

My question is: Has anybody had experience with anything similar? Does anybody know the cell basis vectors compatible with the CHARMM orientation of the RHDO? Are there other conventions out there for the orientation of an RHDO besides SYMMetric and ALIGNed?

Any suggestions at all would be much appreciated.

Dan

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#12613 - 12/06/06 03:03 PM Re: coor conv, RHDO and NAMD [Re: Dan_B]
Dan_B Offline
Forum Member

Registered: 05/23/06
Posts: 35
Loc: Minneapolis, US
In the unlikely case that anybody runs into the same problem:

It turns out that ALIGN (as in COOR CONV SYMM ALIGN) isn't the only other convention for box orientation. In order to have agreement between the CHARMM and NAMD cell basis vector RHDO orientations, I had to do a COOR CONV SYMM ALIGN command followed by a (left-handed) rotation of -arccos(1/sqrt(3)) about the y-axis.. if anybody's interested in more details, send me a message or email and I can try to explain.

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#37504 - 05/16/19 01:05 PM Re: coor conv, RHDO and NAMD [Re: Dan_B]
Antoniel Gomes Offline
Forum Member

Registered: 09/13/18
Posts: 8
Loc: São Paulo, BR
I am interested to understand how you did it.
I sent you a private message.

Thanks

Regards,

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