From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Jan 19 2004 - 08:18:50 CST
Dear NAMD users,
Hello from a new member of this very welcomed list. I just have a
There was a problem with the TIP3 water from Amber in NAMD in the sense
that the angle H-O-H was not restrained (even when rigidbonds all was
used). A solution for this problem was given to me by amber people which
suggested to change the topology file for water in such a way that in
does not contain a H-H bond but rather an H-O-H angle. This worked fine
for me so far and the problem was fixed for earier versions of NAMD.
The disadvantage was that I was using different topology files when
running Amber and Namd
I noticed that the 2.5 version this problem does not exist anymore.
Although the output still warns about the H-H bond the angle H-O-H is
maintained during simulation.
My question is: Is the problem solved now and which was the last NAMD
version which still had this problem?
Thank you very much and I am looking forward to very interesting
subjects on this mailing list
-- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de home tel: ++49-551-9963204
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