Re: [AMBER] nmode memory issue

From: Sushil Mishra <>
Date: Mon, 21 Mar 2011 18:14:52 +0100

There is an article by Ulf Ryde et al, in JCAMD, Volume 23, Number 2, 63-71,
DOI: 10.1007/s10822-008-9238-z
I think this could give you better understanding on using nmode on same
trajectory but by truncating the system.

hope it helps


On Mon, Mar 21, 2011 at 6:01 PM, amit dong <> wrote:

> Hello,
> I am doing entropy calculations on a protein-ligand complex using nmode in
> Amber11. I have MD done on a dimer complexed with ligand. My system has
> ~9500 atoms and I don't have enough memory to do the calculations. The
> system crashes with an error (FATAL: allocation failure in vector() ).
> I am planning to strip off one of the monomer. Is there any quicker way of
> doing it without having to redo the MD with the monomer.
> Thanks
> Amit
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Received on Mon Mar 21 2011 - 10:30:03 PDT
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