[gmx-users] Regarding pdb2gmx and mdrun

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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