Hi, I have tried to run a simulation of 1000 SPC/E water molecules. I have a PDB file containing a 10 by 10 by 10 regular array (cube) of water molecules, each separated by approximately 6 Angstroms. I used pdb2gmx to convert the PDB file to GRO and topology, selecting the OPLS-AA force field and the SPC/E water model. I then used editconf to adjust the box size to a cube of edge length 60 Angstroms (using the option -box 6.0 6.0 6.0 in editconf, because the -box option takes arguments of units in nm, I think). I chose an edge length of 60 Angstroms because by looking at the GRO file, it seems that the largest position coordinate is ~54 Angstroms, so a box with edge length 60 Angstroms should, I think, contain all of the 1000 water molecules.
I then ran energy minimization (steep integrator, emtol = 1000.0 kJ/mol/nm, emstep = 0.01 nm, nsteps = 50000), and steepest descents converged to Fmax < 1000 in one single step. The final potential energy was -3333 kJ/mol, the final maximum force was 11 kJ/mol/nm, and the final norm of force was 8 kJ/mol. It seems a little strange to me that this minimization converged in only one step, but I guess that this means that the water molecules were placed far enough away from each other to begin with. Then I ran an NPT equilibration, and after about 1.5*10^6 steps, the simulation crashed and I got the following error message: --- Program mdrun, VERSION 4.5.4 Source code file: domdec.c, line: 2861 Fatal error: The X-size of the box (4.000392) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (8) times the smallest allowed cell size (0.500000) --- If you have time, do you have any idea about what was the cause of this crash? If I understand correctly, the error message seems to be telling me that (4.000392*1) < (8*0.5). Could it be that my box size is fluctuating too much during this attempted NPT equilibration, leading to the crash? Or perhaps my value of tau_p (tau_p = 2.0 ps) is too large? To summarize, I am trying to do a 5 ns NPT equilibration (5*10^6 steps of 0.001 ps each) with the md integrator, Nose-Hoover temperature coupling, and Berendsen pressure coupling. Should I next try V-rescale temperature coupling instead of Nose-Hoover, since Florian Dommert pointed out to me the other day that (http://lists.gromacs.org/pipermail/gmx-users/2011-May/061716.html) V-rescale tends to be more stable? The complete input file that I used for equilibration is as follows: --- ; npt-eq.mdp ; NPT Equilibration (5 ns) ; NO POSITION RESTRAINT title = OPLS Water NPT equilibration integrator = md nsteps = 5000000 dt = 0.001 nstxout = 250 nstvout = 250 nstenergy = 250 nstlog = 250 ns_type = grid nstlist = 1 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 coulombtype = PME pme_order = 4 fourierspacing = 0.12 tcoupl = nose-hoover tc-grps = system tau_t = 0.1 ref_t = 298 pcoupl = berendsen pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 pbc = xyz DispCorr = no gen_vel = yes gen_temp = 298 gen_seed = 173529 --- Also, the commands I used for equilibration are: grompp -f npt-eq.mdp -c em.gro -p water.top -o npt-eq.tpr -po npt-eqout.mdp mdrun -v -deffnm npt-eq -cpo npt-eq.cpt Thank you very much for your time! I really appreciate it. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
