On 21/10/2011 5:09 PM, aiswarya pawar wrote:
Hi users,
Iam running a minimization on protein complex in vacuum. i have set
the parameters as following-
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
title = Energy Minimization ; Title of run
; The following line tell the program the standard locations where to
find certain files
cpp = /lib/cpp ; Preprocessor
; Define can be used to control processes
define = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator = steepest ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force
< 1.0 kJ/mol
emstep = 0.01
nsteps = 50000 ; Maximum number of (minimization) steps
to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = Protein ; Which energy group(s) to write to disk
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstxout = 1
nstlist = 10 ; Frequency to update the neighbor list and
long range forces
ns_type = grid ; Method to determine neighbor list
(simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short
range forces)
coulombtype = cutoff ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.4 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = no ; Periodic Boundary Conditions (yes/no)
But from this i could write only 2 frames i need to increase the time
frames, what is to be changed in the parameters.
This will write every frame of the EM, but if it only has two steps...
Mark
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