[gmx-users] increase the time frame

aiswarya pawar aiswarya.pawar at gmail.com
Fri Oct 21 08:09:09 CEST 2011

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
emtol        = 1000.0       ; Stop minimization when the maximum force < 1.0
emstep      = 0.01
nsteps        = 50000        ; Maximum number of (minimization) steps to
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,
rlist        = 1.0        ; Cut-off for making neighbor list (short range
coulombtype    = cutoff       ; Treatment of long range electrostatic
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.

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