[gmx-users] Md simulation mdp options error

[Justin Lemkul]

On 4/18/14, 8:55 AM, Ankita Naithani wrote:
> Thank you Justin for your reply. Yes indeed this is a production run. So
> would the following mdp file be okay now?
>
> title        = production MD
> ; Run parameters
> integrator    = md        ; leap-frog algorithm
> nsteps        = 50000000    ; 0.002 * 50000000 = 100000 ps or 100 ns
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout        = 0        ; save coordinates every 2 ps
> nstvout        = 0        ; save velocities every 2 ps
> nstxtcout    = 1000        ; xtc compressed trajectory output every 5 ps
> nstenergy    = 1000            ; save energies every 5 ps
> nstlog        = 1000            ; update log file every 5 ps
> ; Bond parameters
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = all-bonds    ; all bonds (even heavy atom-H bonds)
> constraine
> d
> lincs_iter    = 1        ; accuracy of LINCS
> lincs_order    = 4        ; also related to accuracy
> ; Neighborsearching
> ns_type        = grid        ; search neighboring grid cells
> nstlist        = 5        ; 25 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)
> rlistlong    = 1.0        ; long-range neighborlist cutoff (in nm)
> cutoff-scheme   = Verlet
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range electrostat
> ics
> pme_order    = 4        ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> nstcomm = 10                    ; remove com every 10 steps
> ; Temperature coupling is on
> tcoupl        = V-rescale    ; modified Berendsen thermostat
> tc-grps        = Protein Non-Protein    ; two coupling groups - more
> accurate
> tau_t        = 0.1    0.1    ; time constant, in ps
> ref_t        = 318     318    ; reference temperature, one for each group,
> in
> K
> ; Pressure coupling is off
> pcoupl          = Parrinello-Rahman             ; pressure coupling is on
> for NP
> T
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p           = 2.0                           ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
> compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
> gen_temp    = 318        ; reference temperature, for protein in K
>
>
> grompp -f md.mdp -c npt.gro -p complex.top -o md.tpr?
>
> Could you please advice?
>

The grompp command is incorrect.  As I said before, if you want to preserve the 
work of the previous equilibration, you need to pass the .cpt file from the 
previous step with grompp -t.

Otherwise, provided the cutoffs are correct for your chosen force field, the 
.mdp file looks reasonable.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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