[gmx-users] Topology file for D2O
joys_yu3 at yahoo.com
Tue Mar 27 23:34:33 CEST 2007
Thank you so much for your suggestions. You don't know
how much you guys are helpful.
First with Tsjerk's suggestion of using gmxdump, I got
to know where the problem is. What I changed is
ffgmx.atp and spc.itp. It is useful to pdb2gmx. But
for grompp, it is not enough. I have to change the
file of ffgmxnb.itp. For some reason, grompp reads
this file and determin the mass of all atoms. So far,
I got the mass of hydrogen changed to be 2 in the
readable .tpr file. Of course, I could also see the
mass showed correctly in the log file.
Yes, Andres, I am very interested in the heavy water
poteintial. Please email me the topology and modifed
FF files. Thanks very much.
David, What you thought is very resonable. That's why
Andres said maybe I should consider more specific
heavy water model. But at this moment, I am just
trying to get some preliminary results.
Thank you all,
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