Re: how to restart/continue NAMD run

From: maruthi_at_imsc.res.in
Date: Thu Aug 02 2007 - 04:05:52 CDT

Hi,

  I have begun to learn NAMD quite recently.. So lemme see if my language
suits ur query abt "How to restart" !!

Note: In the below given, run1.* are the files generated by an earlier
simulation .

Make the following modifications to your 'configuration file' to restart
the simulation.

1. Use following tcl commands in "adjustable parameters"
   set previous run1
   set current run2

   set temperature 300 ;# 300 is just arbitrary

2. Keep outputname option as
   set outputname ./file_$current

   This would ensure that the next output files would be written with
   "file_run2" as prefix

3. Uncomment/Include the options
   bincoordinates ./run1.restart.coor
   binvelocities ./run1.restart.vel
   extendedSystem ./run1.restart.xsc

   In this case, the option
   coordinates ./file.pdb

   should be retained, though it is ignored & only "bincoordinates" is used
   for initializing the coordinates for the present configuration.

4. In Input parameters, comment the option
   temperature $temperature

   Because the option "binvelocities" is already specified.
   (Actually specifying "temperature" would result in initializing
    velocities to the present configuration from a Maxwel dist' corres'
    to this temperature;
    AND WE DONT WANT THAT TO HAPPEN AS WE WANT THE SIMULATION TO
    START FROM "binvelocities" now ..)

5. Edit the option
   firsttimestep 92000 ;# 92000 is arbitrary

   92000 is taken from the run1.restart.xsc, which is the number of last saved
   restart configuration of the EARLIER SIMULATION.

6. In Execution script, comment the lines
   minimize 1000
   reinitvels $temperature

   WE DONT WANT MINIMIZATION PROCESS AGAIN (unless the earlier simulation
  did not do it !! )

Note: "set x 30" is equivalent to "x=30" .

Hope it helps you.. please test it before using it on any
important simulation.

Cheers.
Pradeep.

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