I am not understanding the parameters need to change in equilibration and production run conformation files. NAMD tutorials file always use "reinitvels" to equilibrate and that also in a same conformation file. Is the approach OK? Should I just take binvelocities from equilibration file and make a run? Should anything more to be changed? I'm attaching a sample conf file as provided in NAMD tutorial. Experts please help.
There is no as such difference between equlibration and production run in NAMD. All you have to do just make sure your system is equlibrated well enough before collecting the trajectory.
Hey Sk Jahiruddin,
reinitvels resets the temperature to $temperature after minimization has set all atomic velocities to zero; this must be done to run a subsequent equilibration
(http://chemistry.umeche.maine.edu/Modeling/NAMD4.html)
For the dynamics part of the run (the equilibration) you need the reinitvels so you get back velocities corresponding to the temperture you have defined earlier.
Once equilibrated the system, you do not need to minimize, you could just ignore that part, and , as you said, restart using the equilibration velocities.
Check tutorial files in more advanced tutorials, like NAMD on the ion channel membrane protein.
Here, some relevant parts pasted:
# Continuing a job from the restart files
if {1} {
set inputname myinput
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.restart.xsc
}
#the number of steps your previous run (equilibration) ended:
firsttimestep 1262500
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization (with the if {0} you remove this from the list of commands to be executed
if {0} {
minimize 1000
reinitvels $temperature
}
run 1250000 ;# 2.5 ns
Tamás Beke-Somfa,
My basic questions was -
1) Is just the reinitvels enough to equilibriate a system?
2) Is there anything to change in the production run conformation file from equilibration conformation file except reading binvelocitiy from equilibration velocity output file?
Please clarify.
1.) No. You need the "run" command as well.
You need the reinitvels because in this case you want to perform an MD run (as equilibration is technically that) and you want to restore the temp. after a minimization.
2.) you need to read in the restart files, see above, and it is also recommended to provide the number of steps so far performed under the command "firsttimesteps" .
In addition make sure that the minimization part is removed.
It is rather easy, I would suggest that you check a tutorial for NAMD where you would have a production run, such as the 'Membrane Proteins Tutorial'. In that you will find configuration files that show the difference and also the required changes to make after a minimization_equilibration procedure.
Hope this helps,
Tamas
There is no as such difference between equlibration and production run in NAMD. All you have to do just make sure your system is equlibrated well enough before collecting the trajectory.
Tamás Beke-Somfa and Dr. Snehasis Daschakraborty,
Thank you very much for your comments. Things are better clear now.
Tamás Beke-Somfa and Dr. Snehasis Daschakraborty
Please clarify one point more, what does happen if we don't remove the minimize option in production run?
It will only do what you tell it to do. So, if you specify minimization before production, it will minimize the number of steps you ask it to minimize.
Since you minimize the system before the equilibration, you don't need to minimize again before the production run. You just continue the simulation as long as you want.
[lammps MD] What are differences between equilibration RUN and dynamics RUN in lamps
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