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.
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:02 CST