Dear Justin, I ran a short simulation (200ps) with the cool down under NVT and now it seems the system is working. In addition, I removed from the NVT options the tc for all the groups. Thank you, Riccardo El jue, 31-10-2013 a las 08:31 -0400, Justin Lemkul escribió: > > On 10/31/13 8:25 AM, Riccardo Concu wrote: > > Dear all, I'm having some problems during the cool-down process after > > the NVT. > > I'm running the NVT process at a T of 500K for 3ns and everything is > > going well but when I cool down the system blows up. I am running the > > cool down for 100ps, I tried to run the process for longer time (500 ps) > > and decrease nstlist option up to 5 but it seems it doesn't work. The EM > > seems to be fine with very low forces: > > Potential Energy = -3.1736706e+05 > > Maximum force = 2.6573439e+01 on atom 105 > > Norm of force = 3.1027287e-01 > > > > The NVT is compiled with the following mdp: > > define = -DPOSRES ; position restrain the protein and ligand > > ; Run parameters > > integrator = md ; leap-frog integrator > > nsteps = 1500000 ; 2 * 50000 = 100 ps > > dt = 0.002 ; 2 fs > > ; Output control > > nstxout = 10000 ; save coordinates every 0.2 ps > > nstvout = 10000 ; save velocities every 0.2 ps > > nstenergy = 10000 ; save energies every 0.2 ps > > nstlog = 10000 ; update log file every 0.2 ps > > energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- > > ; Bond parameters > > continuation = no ; first dynamics run > > constraint_algorithm = lincs ; holonomic constraints > > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > > constrained > > lincs_iter = 1 ; accuracy of LINCS > > lincs_order = 4 ; also related to accuracy > > ; Neighborsearching > > vdwtype = cutoff > > ns_type = grid ; search neighboring grid cells > > nstlist = 20 ; 10 fs > > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > > ; Electrostatics > > coulombtype = PME ; Particle Mesh Ewald for long-range > > electrostatics > > pme_order = 4 ; cubic interpolation > > fourierspacing = 0.16 ; grid spacing for FFT > > ; Temperature coupling > > tcoupl = V-rescale ; modified Berendsen > > thermostat > > tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- ; two coupling > > groups - more accurate > > Frankly, I'm amazed this was stable. I can't imagine that any system > justifies > this many individual thermostats. > > <snip> > > > Pcoupl = Parrinello-Rahman > > I doubt that you want to try to use Parrinello-Rahman while simultaneously > decreasing the temperature. Even for equilibration runs at stable > temperature, > P-R is a poor choice. I would suggest trying your cooling under NVT, or if > you > absolutely need to do it under NPT, use Berendsen instead; it is much more > forgiving. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ==================================================
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