[gmx-users] InflateGRO methodology deletion radius
jalemkul at vt.edu
Sat Jun 15 13:48:18 CEST 2013
On 6/15/13 3:56 AM, Shima Arasteh wrote:
> In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the lipids, I need to follow the iteration while the cutoff value changed to 0.
> I' d like to know what settings of EM.mdp file are suggested to get the best results of doing shrinking steps?
> When I set the settings as follow, the lipids interfere the peptide however the APL doesn't get the experimental value. So the configuration is not ideal to get through the equilibrium steps.
> define = -DPOSRES
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 100.0 ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to perform
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 0.4 ; Cut-off for making neighbor list (short range forces)
> rlistlong = 6.0
> coulombtype = PME ; Treatment of long range electrostatic interactions
> rcoulomb = 0.4 ; Short-range electrostatic cut-off
> rvdw = 0.4 ; Short-range Van der Waals cut-off
> vdwtype = switch
> rvdw_switch = 0.2
> pbc = xyz ; Periodic Boundary Conditions
> Now, I am wondering if such a settings will serve a proper deletion radius?
No. These settings make no sense to me whatsoever. Don't be confused by the
"cutoff" used by InflateGRO and the cutoff values used in the .mdp file.
InflateGRO uses a search radius to delete lipids, which is specified on the
command line. The cutoff values for the EM and MD runs are dictated by the
force field you are using and are in no way connected to lipid deletion.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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