[gmx-users] segmentation fault in md
Justin Lemkul
jalemkul at vt.edu
Mon Oct 3 13:37:05 CEST 2016
On 10/3/16 2:38 AM, ISHRAT JAHAN wrote:
> Dear all
> I am trying to simulate 3M urea in a water box.when i do the mdrun of pr ,
> i get too many LINCS warning and also segmentation fault(core dumped).
>
> I am pasting my em.mdp and pr.mdp file below-
> em.mdp
> ;
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> cpp = /usr/bin/cpp
> define = -DFLEX_SPC
> constraints = all-bonds
> integrator = steep
> nsteps = 2000
> ;
> ; Energy minimizing stuff
> ;
> emtol = 100
> emstep = 0.01
> nstcomm = 1
> ns_type = grid
> rlist = 0.15
> coulombtype = PME
> rcoulomb = 0.15
> rvdw = .19
These cutoffs are completely nonsensical.
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
>
>
> pr.mdp
>
> ;
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> title = Yo
> cpp = /usr/bin/cpp
> define = -DPOSRES
What is the purpose of position restraints here? You probably don't need any.
> constraints = all-bonds
> constraintalgorithm = LINCS
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 10000 ; total 50 ps.
> nstcomm = 10
> nstxout = 500
> nstvout = 1000
> nstfout = 10
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 2
> coulombtype = PME
> rcoulomb = 2
> rvdw = 2
What force field uses 2-nm cutoffs? Proper use of the force field is a
prerequisite for a sensible simulation.
-Justin
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = V-rescale
> tc-grps = URE Water
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Energy monitoring
> energygrps = URE Water
> ; Pressure coupling is on
> Pcoupl = Berendsen
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
> thanks in advance
>
--
==================================================
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
http://mackerell.umaryland.edu/~jalemkul
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