From: Laura Lopes (laurajoanalopes_at_gmail.com)
Date: Fri Feb 08 2019 - 03:38:55 CST
I just encountered the same problem discussed in this e-mail again, so I
decided to reopen the thread, since I got no explanation to my problem at
To answer Brian, I have a simulation where I need to start from a lot of
different points, decided during the simulation. Because I need to make a
decision before even running my first trajectory, I provide to NAMD a
temperature parameter, otherwise it gives me an error.
Of course I solved this issue by simply giving namdbin files, that are
useless to me, instead of the temperature command. But I really just wanted
to understand what is the origin of this error !
On Fri, Jan 12, 2018 at 9:20 PM Brian Radak <brian.radak_at_gmail.com> wrote:
> 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.
> On Thu, Jan 11, 2018 at 11:36 AM, Laura Joana <laurajoanalopes_at_gmail.com>
>> 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,
>> On Thu, Jan 11, 2018 at 3:26 PM, Laura Joana <laurajoanalopes_at_gmail.com>
>>> 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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