Why have you chosen to get your solvated box 150 mM NaCl? (instead to add just few ion particles in order to neutralize your system).

I mean, I don't know at what extent the ionic strength is well reproduced and, in the meanwhile, what computational artifacts you may introduce.

As for artifacts, there are also numerous examples for the importance of explicit ions in the literature - In my experience a solute that is rather physiological gives quite reasonable results, at least for my protein. I've also checked the direct environment of my water molecule for ions that could cause the observed problems ... they're quite far away so I don't think they're responsible for the crash

Dear Mr. mann

Try using my mdp file. I used it in Gromacs 4.5 without any problem.

best,

HHA

@Daniel - can you post the .mdp file you are using?

@Darrio - ionic strength in simulations can be very critical, though some force fields have known defects. Simply neutralizing the system with counterions is common, but I have seen firsthand that increasing ionic strength can change a proteins' behavior (in a physiologically relevant way!) and for nucleic acids and membranes, the effects are even more pronounced.

@Hamed - that .mdp file would be rather unconventional for OPLS. Typically, cutoffs of 1.0 nm are used, though there is some dispute about what is "best" for OPLS.

Hey Justin,

here's the used .mdp file for energy minimization:

title = xxx

cpp = /lib/cpp

define = -DFLEXIBLE

integrator = steep

nsteps = 75000

nstxout = 2000

nstvout = 2000

nstfout = 2000

nstlog = 2000

nstenergy = 2000

nstxtcout = 2000

nstlist = 10

ns_type = grid

pbc = xyz

rlist = 0.9

coulombtype = PME

rcoulomb = 0.9

vdwtype = cut-off

rvdw = 1.4

fourierspacing = 0.12

PME_order = 4

ewald_rtol = 1e-5

emtol = 0.001

emstep = 0.01

nstcgsteep = 10

energygrps = SOL NA CL

For minimization, nstlist should always be set to 1. You're probably missing interactions with the updates, leading to instability. The fact that it "worked" with a previous version is probably a happy coincidence, but nstlist would be my #1 suspect at this point.

Thank you very much Justin, I'll keep nstlist = 1 during my next simulations.

However, changing it still produces the described crashes -

What I tried next was updating my Gromacs to 4.6.5 - and suddenly everything works fine. I have no idea if I messed something up compiling the 4.5.4 Version, but if anybody observes similar problems with 4.5.4 in the OPLS/AA ff and TIP4P Water maybe updating Gromacs to the latest version can fix this.

Thank you Dario, Hamed and Justin for your support!