Warren Gallin wrote:
Hi,
I am trying to work my way through learning to use GROMACS 4.0.5 for
doing MD simulations of short peptides in solution.
My problem is that several peptides, most strikingly a Serine
10-mer, are exploding during the production run.
I construct the serine polymer in extended form using TINKER, with
neither end capped, then use pdb2gmx, editconv, genbox and genion to set
the forcefield to OPLSAA/L, place it in a box of tip3p water,
neutralized in a .096 M NaCl solution.
I am trying to track down why this is occurring, and the first thing
that seems suspicious is that the initial energy minimization run
reaches convergence with a rather large force remaining on one of the
atoms - the final statement from the EM run is:
Steepest Descents converged to machine precision in 6793 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -4.9731194e+05
Maximum force = 7.1219537e+02 on atom 111
Norm of force = 6.5289087e+00
So I am thinking that with a large initial force on the polymer the
system might be unrecoverably unstable and this is propagating through
the subsequent steps of relaxing the water and the actual MD run to pop
up as an explosion.
If I look at the run log for the MD run, everything seems stable
until the last step, at which point the temperature shoots up and the
serine polymer explodes. Here are the last four steps from the run log:
Step Time Lambda
208200 416.40002 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
9.75158e+03 1.25586e+02 7.62176e+00 -6.45482e+01 1.16773e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
1.80001e+03 6.08872e+04 -4.19574e+05 -4.65971e+04 -3.93547e+05
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
7.77043e+04 -3.15843e+05 1.01418e+06 3.17587e+02 -2.87690e+02
Step Time Lambda
208300 416.60002 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.04345e+04 1.96147e+02 1.55806e+01 -3.31126e+01 1.24787e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
1.80413e+03 6.08422e+04 -4.19233e+05 -4.66893e+04 -3.92538e+05
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
7.77229e+04 -3.14815e+05 1.02114e+06 3.17663e+02 -2.94492e+02
Step Time Lambda
208400 416.80002 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
7.10106e+03 2.06975e+02 1.21357e+01 -2.52705e+01 1.16229e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
1.85247e+03 6.04882e+04 -4.18865e+05 -4.67103e+04 -3.95824e+05
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
7.58806e+04 -3.19943e+05 1.02333e+06 3.10133e+02 -2.90942e+02
Step Time Lambda
208500 417.00002 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
2.30968e+04 4.27637e+02 1.17359e+01 -5.59373e+01 1.39477e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
1.80067e+03 6.20751e+04 -4.20609e+05 -4.67193e+04 -3.79833e+05
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.03323e+05 -2.76511e+05 1.07569e+06 4.22292e+02 2.94766e+02
So my questions are:
1) Am I missing some obvious step in setting up a stable simulation?
2) Is it true that the high internal force present at the end of the
initial energy minimization could be the root of the problem?
3) If so, is there an obvious method for relaxing the system into a
more stable state prior to the main MD run?
What time step are you using? Since you are not using bond-constraints
the time step should be on the order of 0.5 fs.
Warren Gallin
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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