VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Nov 24 2014 - 03:45:07 CST

Hi Maryam,

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
configuration file:

"*margin 2*"

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
script.

Use of margin should fix your problem unless your question was something
else altogether.

Best,
/A

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>
wrote:

> Dear NAMD users:
> Hi
> 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.
> regards:Maryam
> Maryam Atabay
> Ph.D in Nano Computational Chemistry,
> Molecular Simulation Lab, Azarbaijan Shahid Madani University,
> Tabriz,Iran.
> Email: Atabay_at_azaruniv.edu
> 

-- 
Best,
/A