[gmx-users] NVT equilibration

[Justin Lemkul]

On 1/11/14, 11:59 AM, kiana moghaddam wrote:
> Dear GMX Users
>
> I want to equilibrate my system in NVT from 0 to 300 K then in NPT (300K). Is my mdp file in NVT equilibration is correct?
>

Possibly.  "Correct" hinges on whether or not all the settings are appropriate 
for the force field, etc.  You can determine yourself whether or not the heating 
is effective simply by running the simulation.  I suspect that 100 ps of 
dynamics would run faster than the lag time between sending your email and 
receiving this answer :)

-Justin

> define                   = -DPOSRES
> ; Run control
>
> integrator               = md
> dt                       = 0.002 ; ps !
> nsteps                   = 50000 ; total 100.0 ps.
>
> ; Output control
>
> nstxout                  = 500 ; collect data every 1.0 ps
> nstvout                  = 500 ; collect data every 1.0 ps
> nstfout                  = 0
> nstlog                   = 500 ; collect data every 1.0 ps
> nstenergy                = 500 ; collect data every 1.0 ps
> nstxtcout                = 500
> xtc-precision            = 500
> nstcalcenergy            = 10
> energygrps               = DNA_LIG Water_counterions
>
> ; Neighbor searching and short-range nonbonded interactions
> nstlist                  = 5
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
>
> ; Electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.0
>
> ; van der Waals
> vdw-type                 = cut-off
> rvdw                     = 1.0
>
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing            = 0.12
>
> ; EWALD/PME/PPPM parameters
> pme_order                 = 4
>
> ; Temperature coupling
> tcoupl                   = V-rescale
> tc_grps                  = DNA_LIG Water_counterions
> tau_t                    = 0.1     0.1
> ref_t                    = 300     300
>
> ; SIMULATED ANNEALING
> annealing                = single single
> annealing_npoints        = 7 7
> annealing_time           = 0 15  30  45  60  80 100 0 15  30  45  60  80 100
> annealing_temp           = 0 50 100 150 200 250 300 0 50 100 150 200 250 300
>
> ; Pressure coupling is on for NPT
> pcoupl                    = no
>
> ; Dispersion correction
> DispCorr                 = EnerPres
>
> ; generate velocities
> gen_vel                   = yes
> gen_temp                  = 300
> gen_seed                  = -1
>
> ; options for bonds
> continuation             = no
> constraints              = all-bonds
> constraint-algorithm     = lincs
>
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order                = 4
> lincs_iter                 = 1
>

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

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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