VMD-L Mailing List
From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Nov 24 2014 - 03:45:07 CST
You already know the solutions.
Are you asking how to use these ?
If you are -
e.g. to use the margin fix you need to add the following line to your NAMD
useFlexibleCell is off by default so unless you turned it on you don't have
to think on that. If you have turned it on - remove that line from your
Use of margin should fix your problem unless your question was something
p.s. also just to let you know - you should have posted this to the NAMD
mailing list, since its an NAMD related question.
On Mon, Nov 24, 2014 at 10:08 PM, maryam atabay <matabay2010_at_gmail.com>
> Dear NAMD users:
> I want to simulate protein and nanosheet in water with using cuda-enabled
> in the NPT ensamble with fixed-coordinated nanosheet. The minimization and
> heating stages was executed without any error but in the md stage I
> encounter with following 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.
> please help me. I will appreciate the oncoming helps.
> Maryam Atabay
> Ph.D in Nano Computational Chemistry,
> Molecular Simulation Lab, Azarbaijan Shahid Madani University,
> Email: Atabay_at_azaruniv.edu
-- Best, /A