Re: [AMBER] box size and SMD simulation

From: David A Case <>
Date: Sun, 28 Jan 2018 21:44:47 -0500

On Sun, Jan 28, 2018, Ibrahim Said wrote:

> I am using Amber12 and I started to simulate the mechanical response of my
> protein. At the beginning I applied a water box size of 400 x 500 x 950
> Ang. Unfortuantely I got the following message
> "nfft1-3 too large! check on MAXNFFT in ew_bspline.f"
> Then I decreased the dimension of the box to 100 x 300 x 450 Ang. the run
> was Ok till the time reached 800 ps and then the unfolded protein become
> longer than the dimensions of the box. Please, how can I get over these
> problems.

You would need to modify the code to increase the value of MAXNFFT, then
recompile. But two notes:

1. You would probably be better off using pmemd, if possible (there the
variable to change is "gridhi".

2. You should really consider upgrading to the current version of Amber. For
large and time-consuming calculations, the code improvements made over the
past few releases are significant.


AMBER mailing list
Received on Sun Jan 28 2018 - 19:00:02 PST
Custom Search