Hi,
On Fri, Mar 31, 2017 at 12:30 PM, Chris Neale <candrewn.gmail.com> wrote:
> If the issue is simply PBC wrapping during the run then that sounds like
> something that should get fixed in the code at some point, esp given that
> it's called a "restart" file.
An internal solution here is not so simple. I don't see an easy way
you could have the code realize that your system has been imaged with
respect to the reference you've given it. I guess you could have it
detect a very large restraint energy and then do the equivalent of
'autoimage' to the coordinates and see if that helps, but that's a lot
of code duplication and may not always be the correct thing to do. The
solution may be to make sander/pmemd output a more informative error
message when restraints and iwrap are on.
Another alternative is when using positional restraints turn iwrap off
and use netcdf trajectories and restarts. However, in my opinion the
easiest thing to do is make sure you autoimage your restarts when
using position restraints.
-Dan
>
>
> On Fri, Mar 31, 2017 at 12:58 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com> wrote:
>
>> Hiya,
>>
>> You can try reimaging your restart file (with ccptraj) before restarting.
>> It may be that molecules involved in the restraint are in different
>> 'images', which can lead to the behaviour you see upon restarting.
>>
>> Marc
>>
>> On 31 Mar 2017 06:23, "Sadegh Faramarzi Ganjabad" <
>> safaramarziganjabad.mix.wvu.edu> wrote:
>>
>> > Hi Chris,
>> >
>> > I turned off restraints and it works! it's weird. Do you know how I can
>> > restart my simulations without having to turn off restraints?
>> >
>> > Thanks,
>> > Sadegh
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Mar 31 2017 - 10:00:03 PDT
