[gmx-users] segmentation fault in md

[Justin Lemkul]

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

==================================================