On 7/18/17 8:15 AM, S M Bargeen Turzo wrote:
Hey I have been trying to convert S100A8A9(has two chains) to .gro but
after energy minimization I am not getting an integer for the total charge
of the system.
What is the magnitude of this non-integer charge? Did you do anything funny
during pdb2gmx like using -missing?
-Justin
Secondly when I try to do molecular dynamics simulation using these
parameters:
; 0.5 ps NVT production with Langevin thermostat and GB implicit solvent
INPUT
ld_seed = -1 ; Use random seed
# INTEGRATOR
##
define = -DPOSRES
integrator = sd; Langevin thermostat
dt = 0.002 ; Timestep (ps)
nsteps = 250 ; Simulation duration (timesteps)
nstcomm = 250 ; Center of mass motion removal interval
comm_mode = angular; Center of mass motion removal mode
## ENSEMBLE
###
ref_t = 300 ; System temperature (K)
tau_t = 2.0 ; Thermostat time constant (ps)
tc_grps = system; Apply thermostat to complete system
## IMPLICIT SOLVENT
###
implicit_solvent = GBSA ; Generalized Born implicit solvent
gb_algorithm = HCT ; Hawkins-Cramer-Truhlar radii calculation
nstgbradii = 1
rgbradii = 0.0 ; Cutoff for Born radii calculation (A)
gb_epsilon_solvent = 80
gb_saltconc = 0
sa_algorithm = Ace-approximation
sa_surface_tension = 2.25936
### NONBONDED INTERACTIONS
cutoff_scheme = group ; Method of managing neighbor lists
pbc = no ; Periodic boundary conditions disabled
coulombtype = cut-off ; Calculate coulomb interactions using cutoff
rcoulomb = 0.0 ; Coulomb cutoff of infinity
vdw_type = cut-off ; Calculate van der Waals interactions using cutoff
rvdw = 0.0 ; Van der Waals cutoff of infinity
rlist = 0.0 ; Neighbor list cutoff
nstlist = 0 ; Do not update neighbor list
### OUTPUT
nstlog= 50 ; Log output interval (timesteps)
nstenergy = 50 ; Energy output interval (timesteps)
nstcalcenergy = 50 ; Energy calculation interval (timesteps)
nstxout = 50 ; Trajectory output interval (timesteps)
nstvout = 50 ; Velocity outout interval (timesteps)
nstfout = 50 ; Force output interval (timesteps)
I get segmentation fault(11). I don't know what this means. Can you please
help me out?
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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