[gmx-users] OPLS/AA + TIP5P, anybody?

gigo gigo at ibb.waw.pl
Sat Sep 28 04:07:49 CEST 2013

Dear Chris,
Thank you for your reply. I defined a new virtual atomtype (type D) with 
LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and 
played a bit with epsilon till the new LJ repulsion was able to prevent 
the build up of a huge force on the oxygen while interacting with 
dimensionless charged hydrogens. Also, I copied the flexibility 
parameters from tip4p to see if it helps in minimization before I turn 
it into rigid water - it seems that it does. I was able to minimize the 
system with such water. Also, I minimized the system with tip4p and 
replaced it with tip5p with a script. I tried to minimize the system 
afterwards with true tip5p, which did not work. My question is, besides 
the correctness of water model, why do you think it is safe to remove 
the LJ on lone electron pairs in MD? Will it not collapse like in energy 
Best Regards,

On 2013-09-27 05:58, Christopher Neale wrote:
> Dear Gigo:
> I've never used tip5p, but perhaps you could add some LJ terms to the
> opls_120 definition,
> do your minimization, then remove the fake LJ term on opls_120 and run 
> your MD?
> If that doesn't work, then you might be able to minimize your system
> using FLEXIBLE tip3p
> water and then use a script to convert the tip3p into tip5p. I expect
> that you can set 0,0,0
> coordinates for each of the tip5p dummy atoms and that they will get
> correctly positioned
> in your first mdrun step with tip5p.
> Chris.
> -- original message --
> Dear Mark,
> Thank you for your reply. Unfortunately, TIP5P is completely rigid and
> the FLEXIBLE define will not change it. Any other ideas?
> Best,
> g
> On 2013-09-24 23:51, Mark Abraham wrote:
>> You should be able to minimize with CG and TIP5P by eliminating
>> constraints, by making the water use a flexible molecule, e.g. define
>> = -DFLEXIBLE (or something). Check your water .itp file for how to do
>> it.
>> Mark

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