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
==================================================
--
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
