[gmx-users] Weird structure after minimization (membrane proteinsimulation

[Mark Abraham]

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