Re: question about CUDA-enabled

From: Axel Kohlmeyer (
Date: Sat Nov 29 2014 - 19:22:55 CST

On Nov 29, 2014 11:21 AM, "maryam atabay" <> 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.

This question has been asked and answered probably hundreds of times. It
has nothing to do with CUDA. Please do a careful search of the mailing list
archive. Occasionally people give bad advice, because they don't understand
where the message is coming from (your box has shrunk too much and thus a
new domain decomposition has to be done, which cannot be done on the fly).

> regards:Maryam
> --
> Maryam Atabay
> Ph.D in Nano Computational Chemistry,
> Molecular Simulation Lab, Azarbaijan Shahid Madani University,
> Email:

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