Dear all,
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
Hi,
I am not an expert about heavy water -- but it does seem strange to me
to think that you could get "heavy water" just by changing the mass of
the hydrogens in a conventional water model. The *only* thing this
will affect is the kinetic energy and mass of water. Presumably
changing hydrogen to
Hi Joys Yu,
In addition to Tserks comments you might want to use a more specifically
developed heavy water model.
Here is a reference you may find usefull:
An effective pair potential for heavy water - J. Raul Grigera
The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp.
8
Hi Joys Yu,
I'm not exactly sure what is happening and why the mass is not
produced correctly. You could check in the .tpr file using gmxdump
whether the masses are correct there, but given the log, it probably
is not. It is possible that grompp does not read the altered
ffgmx.atp, but uses an or
Dear all,
I would like to do simulation of bulk heavy water
(D2O). So first thing, I need to get the topology file
of D2O. In fact, I would like to use SPC H2O. I just
need to change the mass of H in H2O from 1.008 to
2.016.
I would like to use gromacs force field(#7). So I
revised ffgms.atp. I c
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