[gmx-users] cool down problem

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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