Alok wrote:
Dear Mark & Chris,
Thanks a lot for your help.
As both of you suggested I have increased the tolerence limit of the
bond (using VMD, as described by Chris), after increasing the Dynamic
bond lenth, the structure looks fine.
How long did you have to make the O-H bonds before it looked like all of
them were being "made"?
So it means that during
mimimization, position of water hydrogens are moved further to their
ideal limit. So what could be the possible reason for that?
A broken water model, so check your .top, and the #include file with the
water molecule topology, and pay attention to how the #ifdef mechanism
is working in concert with anything in your "define = xxx" .mdp file entry.
Is this the
problem of my initial structure or that of mimimization parameters
(em.mdp)?
Likely neither, except inasmuch as "define =" selects which bit of the
topology file is being used.
what do you think about my plots from md_run data? Do they look fine or
that could be the root of the problem?
Not sure what you mean here.
Mark
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