[gmx-users] OPLS/AA + TIP5P, anybody?
gigo at ibb.waw.pl
Sun Sep 29 17:13:44 CEST 2013
Authors answered me very quickly. They did not have such a problem, but
I still don't know the details of their input. They used gromacs-3.3, so
I decided to give the old one a try. I did some tests with 3.3.4.
Although the same problem occurred during steep minimization, some
interesting things popped out. When I tried to grompp the system with
plain tip5p for cg minimization, it failed:
"ERROR: can not do Conjugate Gradients with constraints (8484)", even
though I did not set any constraints. The error is the same for tip4p
unless you use flexible model, which tip5p does not have - the water had
to be constrained then. I guess that treatment of virtual sites in
gromacs-3.3 has something to do with this. I noticed, that constraints
make simulations with tip5p more stable. It should not happen, that the
LP virtual atoms are pulled further then the defined 0.7 from the
oxygen, right? I will keep you updated.
On 2013-09-29 04:50, Christopher Neale wrote:
> 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.
> 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
> 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
> posres and constraints turned on.
> 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
>> Also, tip5p has been used successfully with the charmm foce field:
> Yes, there are no dimensionless charged hydrogens there except of these
> on ... tip3p, tip4p and tip5p water.
>> 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:
>> 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
> 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%.
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