[gmx-users] OPLS/AA + TIP5P, anybody?
chris.neale at mail.utoronto.ca
Mon Sep 30 20:47:05 CEST 2013
One a system passes EM and a couple of ps of MD, is it always stable indefinitely? If not, then
something is wrong somewhere.
-- original message --
I put one tip5p molecule in a center of dodecahedral box - 2nm from that
molecule to walls, filled it with tip5p, ran 6000 steps of steep
minimization. After another 2704 steps of cg it converged to emtol 1.0.
I run 100k steps of nvt on this box afterwards
(http://shroom.ibb.waw.pl/tip5p/pure1). But the water is very
capricious. If I ran only 2000 steps of steep, the following cg crashed
after less than 1000 steps because a water molecule could not be
settled. I could not minimize another box, filled only by genbox from an
empty gro file (http://shroom.ibb.waw.pl/tip5p/pure2). I understand that
you have to have some luck if you run a simulation in pbc with rigid
water, which interacts through walls of the box with the other side and
was not well placed. Also, I had several segfaults during minimization
that I was able to avoid only by limiting the number of cores.
I checked distances between OW and LPx on a crashing minimization with a
peptide - 2812 water molecules. Maximum force reached 8.8e+24 in 225
steep steps, but all the 5624 distances were rock solid 0.7A, as
I still did not post the redmine issue, I want to be sure that I am
doing everything correctly.
On 2013-09-29 18:47, Christopher Neale wrote:
> Dear Grzegorz:
> Under no conditions should any of the tip5p geometry change (for the
> standard tip5p model).
> If you find that this is happening, then that is certainly an error.
> You can check if you like by analyzing
> your trajectory. However, flexible bonds will allow the distance from
> the arginine N to the arginine
> H to vary, which my allow a closer approach of the arginine H to the
> tip5p dummy site.
> Did you verify that a water box (no protein) simulates without error?
> Did you post a redmine issue with .mdp , .gro , and .top files?
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