Re: namd with ff99sb

From: Francesco Pietra (
Date: Wed May 29 2013 - 01:27:32 CDT

Hi George:
Thanks a lot for taking so much care about this issue. I adjusted my conf
file for the PNT equilibrated system according to the one you provided for
minimization. This allowed me to uncover the very origin of the problem.
The error comes from the water molecule bound to Zn in the zinc cluster,
not from bulk water. prmtop/inpcrd had been generated with tleap from

Could you suggest a way to treat separately (as far as "rigifBonds" is
concerned) bulk water and the H2O bound to Zn? I.e., rigid bonds for In a
psf/pdb frame, I could use the segname.

All that in the presumption (correct?) that free to vibrate bulk water
slows down the simulation with respect to rigidBonds for bulk water, while
it is correct to allow vibrating H2O bound to Zn.


On Tue, May 28, 2013 at 8:31 PM, George Giambasu <>wrote:

> Francesco - I made few tests on a tip3p water box with namd (cpu and gpu)
> and it seems to work fine. I used tleap from amber-13 distribution. I am
> attaching my files.
> This is how I got the input files:
> source leaprc.ff99SB
> solvatebox WAT TIP3PBOX 20
> saveamberparm WAT wat.parm7 wat.crd
> savepdb WAT wat.pdb
> George

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