From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Nov 29 2014 - 19:22:55 CST
On Nov 29, 2014 11:21 AM, "maryam atabay" <matabay2010_at_gmail.com> wrote:
> 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.
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).
> Maryam Atabay
> Ph.D in Nano Computational Chemistry,
> Molecular Simulation Lab, Azarbaijan Shahid Madani University,
> Email: Atabay_at_azaruniv.edu
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:26 CST