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
minimization?
Best Regards,
Grzegorz
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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