Re: Error applying PME to simulation set up

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 13 2015 - 08:00:00 CDT

On Wed, May 13, 2015 at 1:02 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
> Thanks Norman, the second thing worked! Although the simulation is taking
> longer time to run, but I guess it's better than having no result at all or
> using lumpsum dielectrics overall.

if you want decent performance, do what NAMD told you and restart. it
is in general a *very* good practice to separate multiple
equilibration and then the production simulation steps in to multiple
segments and restart between them.

axel.

>
> Regards
> Sourav
>
> On Wed, May 13, 2015 at 3:38 PM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
>>
>> This most likely isn’t related to PME, but two other options are possible:
>>
>>
>>
>> 1. You cutoff value is close to the periodic cell size.
>>
>> 2. You do NPT and the box shrinks very much. Try setting “margin 5”
>>
>>
>>
>> You might to post your namd input so we can see whats going on.
>>
>>
>>
>> Norman Geist.
>>
>>
>>
>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
>> Of Sourav Ray
>> Sent: Wednesday, May 13, 2015 11:25 AM
>> To: namd-l_at_ks.uiuc.edu
>> Subject: namd-l: Error applying PME to simulation set up
>>
>>
>>
>> Hello
>>
>>
>>
>> I tried running a helical protein structure equilibriated in water and
>> ionized to 0.1 mol/L with NaCl. However, I encountered an error
>>
>>
>>
>> "FATAL ERROR: Periodic cell has become too small for original patch grid!
>>
>> Possible solutions are to restart from a recent checkpoint, increase
>> margin, or disable useFlexibleCell for liquid simulation."
>>
>>
>>
>> while applying PME electrostatics whereas setting a dielectric value to
>> say 15 is working fine.
>>
>>
>>
>> Can anyone here provide certain insight into this issue?
>>
>>
>>
>> Thanks
>>
>> Sourav
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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