Hi Myunggi,
>From my reading of your input you are trying to do umbrella sampling
(IUMB=1) using a restraint between atoms 1 and 6 by changing the
equilibrium value of the restraint from 8 Ang at lam=0 to 2.5 Ang at
lam=1 while keeping the K value fixed at 5 kcal/mol.
If this is the case you don't need to set ITOR=1 as you have done but I
don't think that this is the problem.
Things to check.
You are starting your simulation at lam=1 so the crd that you give
should probably correspond to the atoms 1-6 at a distance of 2.5 rather
than 8. Otherwise you can swap the 8 and the 2.5 in the input and you
will probably be going in the right direction.
You are starting with no velocities (ntx=1) and a target temp of 300.
Personally, I would avoid this as the system will be trying to
equilibrate while you are collecting data.
I don't have a great deal of experience with umbrella sampling but I'm
not sure that a force constant of 5 kcal/A will be enough to get you
sampling the whole distance range that you want. You could experiment
with increasing this to see if it helps.
Otherwise you can try ITOR=2 (constraints) to see if you can actually
get the distance changing and the problem is not somewhere else. If that
works then you know the problem is with the umbrella potentials.
Hope that is of some help.
Good luck.
--
---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 77740
Fax.: +49 (0)89 2180 77738
e-mail: David.Smith.cup.uni-muenchen.de
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Received on Thu Feb 26 2004 - 09:53:00 PST
