From: Abhishek Tyagi (atyagiaa_at_connect.ust.hk)
Date: Sat Nov 29 2014 - 11:04:55 CST
I think you must reduce your tilmestep to 1 and for NPT ensemble, try this, and please post your config file
cheers
Abhi
> On 30 Nov, 2014, at 12:19 am, 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 <mailto:Atabay_at_azaruniv.edu>
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