From: Ashutosh Shandilya (scfbioiitd_at_gmail.com)
Date: Tue Mar 06 2018 - 15:41:54 CST
Thanks, I used margin 3 after removing langevin piston it worked for (*nvt.in
<http://nvt.in>*) but when I am trying to run npt it is still gives the
same error (*Periodic cell has become too small for original patch grid!*).
Attached are my input files, kindly have a look if I am missing something.
Many thanks,
Ashutosh
On Tue, Mar 6, 2018 at 2:50 AM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:
> You can just add a line:
>
>
>
> margin 3
>
>
>
> to the namd input file. This will mostly prevent namd from aborting on
> large box shrink on the cost of performance. Therefore, after the 1st
> initial shrink, you can restart the npt without margin since the box won’t
> shrink that much again. Actually the reason why it shrinks so much
> initially, is that the solvation tool you used (but almost all do) gave the
> system a too small density.
>
>
>
> Norman
>
>
>
> *Von:* Ashutosh Shandilya [mailto:scfbioiitd_at_gmail.com]
> *Gesendet:* Montag, 5. März 2018 22:04
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Betreff:* Re: namd-l: periodic cell has become too small for original
> patch grid
>
>
>
> Thanks for your help. I switched off the Langevin piston (nvt.namd) and
> it ran fine but now when I am switching to npt stepwise it has again the
> same error. I am restarting with old coordinate, vel, xsc but still, the
> problem persists. Could you explain how to you margin or any other
> modification in the input file? I want to run a targeted MD and production
> input file is also attached.
>
> Attached are my input files. Kindly have a look and suggest.
>
> Many thanks,
>
> Ash
>
>
>
> On Mon, Mar 5, 2018 at 3:17 AM, Norman Geist <norman.geist_at_uni-greifswald--001a1140f5e6aadcc20566c54f46--
--001a1140f5e6aadcc60566c54f48--
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