[gmx-users] MD run failed..
hanniballecter13 at gmail.com
Fri Feb 20 19:02:02 CET 2015
Just out of curiosity what does -0.1 actually mean?
On Fri, Feb 20, 2015 at 8:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 2/20/15 6:51 AM, Kalyanashis Jana wrote:
>> Dear all,
>> I am doing an MD simulation of a protein system. Energy minimization step
>> has been completed smoothly but the position restraint MD run is not
>> running properly(after 500-900 steps have been stopped automatically).
>> it has not shown any error or anything. I have used a drug molecule in the
>> cavity of the active site.
>> When the box size was 10 X 12 X 25, it was run only 100 steps and with 15
>> 15 X 28 box size it was run 500-900 steps. I could not understand what is
>> the problem. Can anyone please help me?
>> The pr.mdp file is
>> cpp = /usr/bin/cpp
>> define = -DPOSRES
>> constraints = all-bonds
>> integrator = md
>> dt = 0.001 ; ps !
>> nsteps = 1000000 ; total 1000.0 ps.
>> nstcomm = 100
>> nstxout = 250 ; ouput coordinates every 0.5 ps
>> nstvout = 1000 ; output velocities every 2.0 ps
>> nstfout = 0
>> nstlog = 100
>> nstenergy = 100
>> nstlist = 100
>> ns_type = grid
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdwtype = cut-off
>> rvdw = 1.0
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 6
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> ; V-rescale temparature coupling is on
>> Tcoupl = V-rescale
>> tau_t = 1.0 1.0 -0.1 1.0 1.0
>> tc_grps = SOL NA protein DRG CL
>> ref_t = 300 300 300 300 300
> This thermostat setup is nonsensical.
> ; Pressure coupling is on
>> pcoupl = berendsen ; Use Parrinello-Rahman for research work
>> pcoupltype = isotropic ; Use semiisotropic when working with
>> tau_p = 2.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> refcoord-scaling = all
>> ; Generate velocites is on at 300 K.
>> gen_vel = yes
>> gen_temp = 300.0
>> gen_seed = 173529
>> Thanks in advance,
>> Kalyanashis Jana.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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