Re: reinitatoms

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
sentence:
"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
/home/silva-ll/cyclodextrine/ic/cycloA_A.vel
< 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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