From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Sep 02 2010 - 18:16:08 CDT
Although you neglected to provide your entire configuration file, I would guess that you commented out the wrapAll or wrapWater line as well. This only affects visualization of the trajectory though and not the actual dynamics.
On Sep 2, 2010, at 5:26 PM, Parisa Akhski wrote:
>
> 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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