Re: reinitatoms

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Jan 12 2018 - 14:20:14 CST

Why do you need to use reinitatoms here? I would have though that this
would only be useful after having run dynamics for some period of time.

Brian

On Thu, Jan 11, 2018 at 11:36 AM, Laura Joana <laurajoanalopes_at_gmail.com>
wrote:

> 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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