RE: [AMBER] issues with pmemd

From: Ross Walker <>
Date: Tue, 30 Mar 2010 14:05:04 -0700

Hi Ganesh,

> Thanks for the message. I was unsuccessful in using solvatebox. The
> protein
> which is a fibrin has a y dimension of
> around 250 A. It is made of 411 amino acids. The other dimensions are
> around
> 62 A each. I used around 30000 atoms with packmol program and saw that
> the
> protein was completely immersed.
> Is there a way I could still make use of solvate box. Even if i did I
> would
> be having around 2 million atoms. I could resort to
> implicit solvent or work with a few explicit solvents.
> However I a compiled version of sander on my desktop and it was
> performing
> the minimization "okay" but slow. I would
> very much like to solvate this system. Could I get around with a few
> water
> molecules (explicit).

In this case simply edit the value of gridhi in
amber10/src/pmemd/src/mdin_ewald_dat.fpp and change it to 512 then recompile
PMEMD and you should be good. Just be aware that if you run MD with such a
long system, with a rectangular box (as opposed to a truncated octahedron)
that it may rotate in the box so that it ends up sticking out of the sides.
This would be bad so you will have to find a way to deal with this. You
could devise some restraints that would prevent it from rotating but you
will have to be careful that this doesn't disrupt the dynamics that you are
interested in.

As a side note the 999,999 atom limit in both sander and pmemd will be
removed in the upcoming AMBER 11 and the limits on the maximum FFT
dimensions also increased.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Tue Mar 30 2010 - 14:30:02 PDT
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