Dear Gigo:
that's a good comprehensive testing and report. Please let us know
what you find out from those authors.
Their paper was short on methods (unless I missed it... I didn't check
for any SI), so perhaps they did something
non-standard and didn't report it.
I think at this point it is a good idea for you to file a redmine
issue. It's not a gromacs error per se, but
if this is true then pdb2gmx or grompp should give a warning or error
for the combination of oplsaa and tip5p.
Chris.
gigo gigo at ibb.waw.pl
Sun Sep 29 00:59:42 CEST 2013
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Dear Chris,
I am really grateful for your help. This is what I did, with additional
LJ terms on LP1 and LP2 of tip5p:
- 5000 steps of steepest descent with positions restraints on protein
and flexible water (flexibility like in tip4p),
- 5000 steps of steep, no restraints, flexible water,
- 5000 steps of cg, flexible water,
- 100000 steps of MD with posres and constrained bond lengths, very
weak
temp coupling (v-rescale), starting without generating of initial
velocities, so its heating very slowly to 300K, no pressure coupling
- 100000 steps of MD with posres, no constraints, v-rescale, nvt
- 100000 steps of MD, no posres, nvt,
- 100000 steps of MD, v-rescale, Berendsen pressure coupling,
- 100000 steps of MD, v-rescale, Parrinello-Rahman pressure coupling.
Output of this chain, after removing LJ from LP, became input for 4
simulations just like the last one from the above chain, with or
without
posres and constraints turned on.
Results:
1) Posres off, constraints off :
"step 0"
"WARNING: Listed nonbonded interaction between particles 1157 and 1163"
<== Why does it say "particles" and not "atoms"? Nevermind, its lysine
on the surface of the protein, one of atoms is dimensionless hydrogen.
(...)
"step 63: Water molecule starting at atom 7923 can not be settled."
(...)
"Segmentation fault"
2) Posres off, constraints on :
Warning like above + LINCS warnings, all for charged aminoacids on
surface of the protein
Segfault at step 63
3) Posres on, constraints off, had to add refcoord_scaling = COM :
"WARNING: Listed nonbonded interaction between particles 3075 and 3079"
<== arginine on the surface, dimensionless hydrogen
4) Posres on, constraints on, refcoord_scaling = COM :
Same warnings, several other positively charged dimensionless hydrogens
listed, waters could not be settled, segfault.
I tried to run few other peptides and proteins with tip5p, 100% of
crashes.
Also, tip5p has been used successfully with the charmm foce field:
http://pubs.acs.org/doi/abs/10.1021/ct700053u
Yes, there are no dimensionless charged hydrogens there except of these
on ... tip3p, tip4p and tip5p water.
(...)
http://pubs.acs.org/doi/abs/10.1021/ct300180w
(...)
Are you using halogens with oplsaa-x?
No, I use OPLSAA distributed with Gromacs.
Standard oplsaa (non-x) and tip5p seem to be a fine combination:
http://www.sciencedirect.com/science/article/pii/S0006349507713863
you might want to contact the authors of that paper to see if they
ever had such problems.
Thank you, I will ask them. I am starting to be sure, though, that it
is
not possible to run any simulations with tip5p and proteins (containing
arginine for example) without some tricks, strengthening/constraining
bonds at least. It happened during the minimization, that the distance
between HHxy and NHx in arginine grew up to 1.48A, while HHxy was
landing on LP of the water. Repeatability is 100%.
Regards,
Grzegorz
