simulation cell enlarging too much after restart

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Thu Sep 02 2010 - 17:26:40 CDT

Dear NAMD users,

I am running a simulation on a DNA system. After about 10 ns, I have to restart the simulation due to time limit.
According to NAMD tutorial and also mailing list, I have the configuration file as below:

Since I am using .restart.xsc, I commented out the periodic boundary condition part (but, kept PME). But, after running the restart job, water molecules go beyond the cell so that the cell volume is almost 10 times bigger than before. My guess is that it is related to the PBC but, I am not sure how to solve this problem.

## Input files
structure dna_wb.psf
coordinates coorequil5-a.pdb
########################################################
set temperature 310
set outputname uncons-cont
# Continuing a job from the restart files
 if {1} {
binCoordinates uncons.restart.coor
binVelocities uncons.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem uncons.restart.xsc
 }

Any idea would be really appreciated.

Parisa

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