Re: Npt lipid simulation with electrostatics 2

From: Jeff Comer (
Date: Fri Feb 17 2017 - 10:31:43 CST

Usually the problem causing "system too small for periodic patch grid"
is that the initial size of the system doesn't correspond well to the
equilibrated size. If you get this error after a many steps, you can
just restart NAMD from the last frame of the failed run. Just use
something like restartFreq 100 and restart after the size has changed
a bit.

If the initial size and equilibrated size are very different, you may
want to change your initial size and rerun the minimization.

Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Thu, Feb 16, 2017 at 4:46 PM, Life Sciences Inc
<> wrote:
> Hi All
> I am facing a problem with Npt for the lipid system while giving 2 as full
> elect frequency in namd. It is returning an error of periodic cell becoming
> too short, I tried with 1 and the job is running fine. I have tried
> solutions given in the namd forum but still unable to run the job with 2. I
> tried changing margin tried also running the job with small time step but
> nothing is working. Althought with NVT simulation lipid system is running
> with 2 value but as I switch back again to NPT somehow electrostatics with 2
> is not working. Can this problem be solved ?
> Thanks in advance

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