On 6/15/13 3:56 AM, Shima Arasteh wrote:
Hi,
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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