[gmx-users] MDP

[kia balali]

Dear All,
I am trying to run an MD simulation on a mixed lipid bilay...
box of SPC. I have ran a steep EM on the system (which con...
. The potential energy of the system is now 2.3 x 10e-7.
>reading the literature that I should use PME and not Reaction field like 
>older explicit bilayer simulations. I think my fourier spacing is ok. In 
>addition, my total system charge is zero. I do however have a Na counterion 
>present for a Phosphatidyl Glycerol headgroup!
>
>However, after 40 steps of MD I get the following error messages followed 
>by a crash! I did get 1 warning from grompp {unkown left hand rlist in 
>parameter file!)
>
>I then try going for an mdrun.....this is the result :-(
>
>warning: Pressure Scalling more than 1% mu : 1.0816 1.0816 1.0816
>fatal error : ci = -2147483648 should be in 0 .. 21141 [file nsgrid.c, line 
>210]
>
>Not surprisingly, this fatal error occurs on both NODES!!!!
>
>Below is a copy of my MDP file.....
>
>My PC runs linux, has a dual athlon processor and runs MPI LAM.
>
>Any help/suggestions will be much appreciated!!!!!!!!!!!!!;-)
>
>; PREPROCESSING
>title                  = DOPC
>cpp                    = /lib/cpp
>include                = -I
>
>; RUN CONTROL
>integrator             = md
>tinit                  = 0
>dt                     = 0.002
>nsteps                 = 1000000
>nstcomm                = 10
>
>; LANGEVIN DYNAMICS
>
>; ENERGY MINIMIZATION
>emtol                  = 100.0
>emstep                 = 0.5
>nstcgsteep             =
>
>; SHELL MOLECULAR DYNAMICS
>
>; OUTPUT CONTROL
>nstxout                = 500
>nstvout                = 0
>nstfout                = 0
>nstlog                 = 1000
>nstenergy              = 1000
>nstxtcout              = 1000
>;nstcomm                = -1
>
>; NEIGHBOR SEARCHING
>nstlist                = 10
>ns_type                = grid
>pbc                    = xyz
>rlist                  = 0.9
>
>; ELECTROSTATICS AND VDW
>coulombtype            = PME
>rvdw                   = 0.9
>rlist                  = 0.9
>rcoulomb               = 0.9
>fourierspacing         = 0.12
>pme_order              = 4
>ewald_rtol             = 1e-5
>;coulombtype            = Reaction-Field
>;rcoulomb               = 1
>;epsilon_r              = 1.01
>vdwtype                = Cut-off
>;rvdw                   = 1
>;dispcorr               = no
>
>; TEMPERATURE COUPLING
>tcoupl                 = berendsen
>tau_t                  = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
>ref_t                  = 300 300 300 300 300 300 300 300
>tc_grps                = OLA OLB DPC OLC OLD DPG Na  SOL
>
>; PRESSURE COUPLING
>pcoupl                 = berendsen
>pcoupltype             = isotropic
>tau_p                  = 0.1 0.1
>compressibility        = 4.5e-5 4.5e-5
>ref_p                  = 1.0 1.0
>
>; SIMULATED ANNEALING
>annealing              = no
>
>; VELOCITY GENERATION
>gen_vel                = no
>
>;BONDS
>constraints            = none
>
>
>Kia Balali-Mood
>PhD student
>Dept. of preclinical Veterinary Sciences
>Laboratory of Membrane Biophysics
>The Vet School
>College of Medicine & Veterinary Medicine
>University of Edinburgh
>Summerhall




Kia Balali-Mood
Dept. of preclinical Veterinary Sciences
Laboratory of Membrane Biophysics
The Vet School
Faculty group of Medicine & Veterinary Medicine
University of Edinburgh
Summerhall




_________________________________________________________________
Surf the Web without missing calls! Get MSN Broadband. 
http://resourcecenter.msn.com/access/plans/freeactivation.asp