[gmx-users] Weird structure after minimization (membrane protein simulation)

Mark Abraham mark.abraham at anu.edu.au
Sun Feb 3 14:28:12 CET 2008

> Dear Mark and Chris,
> Thanks a lot for your suggestions which gave me idea to solve the problem.
> I have run the minimization again, without the FLEXIBLE water molecules.
> After the minimization, structure looks perfectly ok to me. please have a
> look at the new snapshoot.
> http://i269.photobucket.com/albums/jj58/gromacs/after_em.jpg

Looks fine.

> It is just my speculation that because I am using the TIP4P water model,
> which has dummy atom (-1.04 charge), it might be possible that due to this
> water hydrogen's (+0.52 charge) are attracted to the dummy atom of nearby
> water molecules. That's why if I closely observed the structures (after
> minimization using flexible water model) then, some water molecules
> aggregates, and leave some vacuum at other places, that's why structure
> was
> looking weird. It is just my speculation please correct me if I am missing
> something.

It's a reasonable theory, but it seems unlikely that you're the first
person to have encountered this problem, if indeed it is the only problem.
Still, there's not much need for flexible waters in your EM, so you can
keep them rigid and go on with life. I'd do that with a clean install, in
case something weird you've forgotten about is causing the problem.

> I have also checked the bond and angle energy values and when I was using
> the flexible water model it deviate a lot. For bond energy it increases
> 8.88556e+04 to 4.10925e+07 and for angle energy 3.60214e+04 to 1.09253e+06
> these energy compensated by short range Coulomb which changes -1.65898e+07
> to -1.71941e+08 .

Well that lends credence to your theory, so perhaps you should look at the
paper that describes the development of TIP4P and see if they recommend
anything. I've not used TIP4P, so know nothing much about it.

> Without flexible water molecules there is no such huge deviation from the
> original value.Also during the equilibration run I have not observed any
> LINCS warnings. I am hoping my problem is solved now :-)

Good :-)


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