From: Cristina Rodríguez (crisrod_at_chem.ubc.ca)
Date: Mon Feb 14 2011 - 19:08:07 CST
Dear NAMD users!!!!
Along many tutorials and papers one could find some basic protocol for running a MD simulation, i.e.
1. Minimization
2. Heating
3. Equilibration
4. Production
The second step (Heating) is recommended to take the system in a gentle way from 0 K to the desired temperature running short simulations in steps of low increments.
On NAMD there are several ways to handle T control:
a) Changing velocities and/or
b) reassigning temperature (I came upon this thread in NAMD-L archive: http://ftp.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8204.html)
As an example, in case you use (a) the config file contains a loop to increment the temperature in step:
for {set TEMP 0} {$TEMP <=310} {incr TEMP 5} {
langevinTemp $TEMP
output md.$TEMP
run 2000 ; #2ps
}
On contrary, if you use (b) the config file contains something like that:
reassignFreq 5
reassignTemp 0
reassignIncr 1
reassignHold 310
Which method is best suited for this purpose? Which are the main differences between them?
Any comment would be really appreciated!!!!!
Regards,
Cristina
------------
Cristina Rodríguez-Rodríguez, PhD
Department of Chemistry
University of British Columbia
Lab D419 - 2036 Main Mall
Vancouver, BC
Canada V6T 2A3
Email: crisrod_at_chem.ubc.ca
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