From: Laura Joana (
Date: Thu Jan 11 2018 - 08:26:28 CST

Dear all,

I'm having a problem involving the use of the command *reinitatoms file*.
I run two simulations, almost the same configuration file, the only
difference is that for the first one I call *bincoordinates, binvelocities
and extendedsystem* with some checkpoint and the other I use the
*temperature* command. For both I call *reinitatoms file* (some other
checkpoint) before any run command. I expected no difference between those
simulations. The problem is that the first one runs normally and the second
give me an error and do not even run ! The error is "Periodic cell has
become too small for original patch grid".
So the question is: what is the difference in using *reinitatoms file*
after *bincoordinates, binvelocities and extendedsystem* and after the
*temperature* command ? Shouldn't NAMD just read *file.coor, file.vel and
file.xsc* and ignore the other previous commands ?
Best regards,


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