Re: TMD in NAMD: cannot reach target

From: Thomas Gaillard (
Date: Thu Nov 01 2007 - 14:00:17 CDT

On Thu, Nov 01, 2007 at 11:13:23AM -0700, lily jin wrote :
> Dear all,
> I am trying to run TMD in NAMD. The first time I let it run 10000time steps, but it couldn't reach the target conformation rff1. The second time I let it run 15000 time steps, it past the target conformation, but never matchs the target conformation. TMD ends at:
> case 1(10000 steps):
> TMD 9998 0.00134302 3.73678

Hi Lily,

The current RMS cannot follow the current RMS: you should try first to
increase the force constant TMDk to 1000000 for example.

If it is not working, are you running in parallel? If yes, you should try it in
monoprocessor instead, I reported a bug about it. I don't know if the
problem has been solved.


Thomas Gaillard
Laboratoire de Biophysicochimie MolÚculaire
Institut de Chimie LC3 - UMR 7177
UniversitÚ Louis Pasteur
4 rue Blaise Pascal
F-67000 Strasbourg
phone: +33 (0)390 241 493
fax: +33 (0)390 241 490

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