[gmx-users] Weird structure after minimization (membrane proteinsimulation
Mark.Abraham at anu.edu.au
Wed Jan 30 07:48:00 CET 2008
> 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
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.
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