On Wed, Feb 15, 2012, Dilraj LAMA wrote:
>
> So my understanding from the mailing list suggest me that
> either options should be ok with their respective pros and cons. I am
> a bit inclined towards using "iwrap=1" for my simulation. However I am
> concerned just in case I encounter some issues later resulting in
> loss of resource and time.
The problem with iwrap=0 on long trajectories is that the system can diffuse
so far (translational motion) that the coordinates no longer fit into the
space allotted to them in the restart file. Then you get the dreaded "****"
entries, and the restart file is useless.
In the next release, we will support binary (netcdf) restart files, which
won't have the problems of the formatted restart files. But for now, setting
iwrap=1 is generally a good idea if you are planning runs spanning more than a
few nanoseconds.
The main problem with iwrap=1 is that it doesn't provide any flexibility about
*how* to do the wrapping. So the result is often flawed, and you have to
"re-wrap" with ptraj/cpptraj. But generally, the virtues of setting iwrap=1
outweigh the disadvantages.
....dac
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Received on Wed Feb 15 2012 - 05:30:03 PST
