AMBER Archive (2004)

Subject: RE: AMBER: ptraj

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Mar 01 2004 - 17:25:41 CST

Dear Carsten,

What are you wanting ptraj to do? Process an mdcrd file? And if so, how many
frames.

A simple rms fit to the initial structure for 4,600 atoms x 1,000 frames
should take less than a minute on a 3GHz P4.

Please be more specific - include your input file with the email if you can.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Carsten Detering
> Sent: 01 March 2004 09:23
> To: amber_at_scripps.edu
> Subject: AMBER: ptraj
>
> Hello Ambers,
>
> I would like to know how long I should expect a ptraj
> calculation (4600
> atoms, noimage) to last approximately. I use a dual Xeon with
> 4Gbyte memory.
>
> thanks in advance,
>
> Carsten
>
>
> --
>
> Carsten Detering
> University of Washington
> Seattle, WA 98195
> Fon 206.543.5081
> Fax 206.685.8665
>
>
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