Hi everyone,<br><br>in the last weeks I've been trying to run a simulation with Gromacs 4.0.5 and the force field ffamber99.<br>The protein is albumine (BSA, bovine serum albumine), so it's a very big one (570+ residues).<br>
The solvent is tip3p.<br>After an energy minimization run and a position restraint run, I start with the "real" simulation. Invariably, it crashes after 1 ps with the error message:<br><br>t = 1.000 ps: Water molecule starting at atom 42031 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br><br>I've searched in the mailing list and I've tried many of the solutions you proposed:<br><br>- I looked at the water molecule with the problematic atom to see if it was interacting in some weird way with the protein (I put ntsxout = 1 in order to have many more frames); but it isn't so, since that molecule is only one of the many solvent molecules that (at least in the first ps) stay far from the protein<br>
- I tried to run a longer and stronger minimization: so I increased the number of steps (from 10000 to 20000) and I decreased emtol (from 100 to 1), but nothing changed<br>- I tried to increase the box dimensions; in editconf I put -c 1.2 (instead of 0.7), but nothing changed.<br>
- I checked the stepXXXb.pdb and stepXXXc.pdb that mdrun created after the crash, but I didn't see anything strange in them.<br>- I did a longer position restraint run (3 ns instead of the usual 200 ps) but nothing changed... I was hoping that it would stabilize the water, but I think the problem is not that.<br>
<br>Even though the energy minimization doesn't show any problems, I think that's the crucial part; as someone said in another message, the problem doesn't really involve the water molecule that cannot be settled, but other atoms in the protein with big forces that in some way collide with the water molecule... am I right?<br>
In this case, deleting the problematic water molecule could help? I thought it would be useless, since that molecule is not close to the protein at all...<br><br>Here you have the em.mdp and the md.mdp, if you want I can also paste the pr.mdp .<br>
<br>title = hsacyx<br>cpp = /lib/cpp<br>define = -DFLEX_SPC<br>constraints = none<br>integrator = steep<br>dt = 0.002 ; ps !<br>nsteps = 20000<br>
nstlist = 10 <br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>
fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 6<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 1<br>emstep = 0.01<br>
<br><br><br>title = hsacyx <br>cpp = /lib/cpp <br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 7500000; total 15000 ps.<br>
nstcomm = 1<br>nstxout = 2500<br>nstvout = 0<br>nstfout = 0<br>nstlist = 500 <br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>
rcoulomb = 0.9<br>rvdw = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 6<br>ewald_rtol = 1e-5<br>
optimize_fft = yes<br>; Berendsen temperature coupling is on in three groups<br>Tcoupl = berendsen<br>tau_t = 0.1 0.1 0.1 <br>tc-grps = protein sol NA+<br>
ref_t = 300 300 300<br>; Pressure coupling is on<br>Pcoupl = berendsen<br>pcoupltype = isotropic<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br><br>I really don't know what else I could do... if someone has an idea, I would be glad to hear it.<br>
Thank you<br><br>Simone Cirri<br>PhD student at the Structural Biology Lab of University of Siena, Italy<br>