From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Thu Jan 11 2018 - 10:36:31 CST
Dear all again,
Sorry for the two e-mails, but I decided to explore the issue a bit more.
Looking at the NAMD 2.12 release features I guess the problem is in this
"The patch grid and other simulation paramters are *not* changed, so the
dimensions of the new and old structures must be compatible." (under Ability
to reload molecular structure without restarting).
Making a diff with my two logfiles I get this:
< Info: PATCH GRID IS 3 (PERIODIC) BY 3 (PERIODIC) BY 1 (PERIODIC)
< Info: PATCH GRID IS 2-AWAY BY 2-AWAY BY 1-AWAY
< Info: Reading from binary file
< Info: REMOVING COM VELOCITY -0.0432567 0.00241296 0.0339374
< Info: LARGEST PATCH (0) HAS 417 ATOMS
--- > Info: PATCH GRID IS 4 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC) > Info: PATCH GRID IS 2-AWAY BY 1-AWAY BY 1-AWAY > Info: REMOVING COM VELOCITY 0.087986 -0.125532 0.0988174 > Info: LARGEST PATCH (3) HAS 237 ATOMS Does anyone know if I'm in the good road to find out what is the problem ? Best regards, Laura On Thu, Jan 11, 2018 at 3:26 PM, Laura Joana <laurajoanalopes_at_gmail.com> wrote: > 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, > > Laura >
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