Re: Error applying PME to simulation set up

From: Sourav Ray (souravray90_at_gmail.com)
Date: Wed May 13 2015 - 06:02:51 CDT

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.

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
>

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