[gmx-users] increase the time frame

[Mark Abraham]

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