your problem is that you are averaging over a period of time when the water
is moving, so the average is unphysical. average positions of water are
typically not informative because of motion and exchange with bulk water.
you're much better off looking at water densities using ptraj's grid
command.
On Mon, Nov 22, 2010 at 11:31 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> Dear amber users,
>
> I am doing a simulation of DNA in water using Amber 9.0 version.
> I am try to get a average structure of solvated DNA over the last 3 ns with
> an aim to see the average position of water molecules within the first
> salvation layer of DNA, using the the following script in Ptraj
>
>
>
>
> ********************************************************************************
> trajin ../27md.crd
> trajin ../28md.crd
>
>
> center :289-300 mass origin
> image origin center
> center :289-312 mass origin ( 289 to 312 for DNA molecules)
> image origin center
>
> rms first mass out rms.dat :289-312
>
> average average.pdb pdb
>
>
> ***********************************************************************************
>
>
> But in the average structure water forms big blob in the center of the
> DNA.
> When I try to do few steps of minimization, run terminated with an error
> as
> shown below....
>
> * NB pairs 5449 26125589 exceeds capacity ( 26125624)
> SIZE OF NONBOND LIST = 26125624
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>
>
> Can anyone help me to figure out what went wrong with the calculation?
>
>
> Thanks in advance
>
>
> Sincerely
> Aneesh
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>
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Received on Mon Nov 22 2010 - 09:00:07 PST
