[gmx-users] Md simulation mdp options error

[Ankita Naithani]

Sorry for the typo.

grompp -f md.mdp -c npt.gro -p complex.top -t npt.cpt -o md.tpr

This is fine, right?

Thanks very much Justin for confirming the mdp file opions..


On Fri, Apr 18, 2014 at 2:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
Ankita Naithani