Re: [AMBER] stripWAT command and saving a new trajectory

From: Jason Swails <>
Date: Mon, 10 Jan 2011 18:41:31 -0500


A couple comments:

1. If you strip waters, you'll have to create a new topology file that
doesn't have the waters in it in order to analyze those trajectories. With
this new topology file, you can do exactly what you asked.

2. Strongly consider using NETCDF formats. They are compressed in size (not
quite as small as gzipped files, but similar), and much much much (add some
more muches) faster to process (and if you write them straight from
sander/pmemd, they have machine precision numbers, which is significantly
better than the truncated, formatted ASCII output of typical MDCRD files).
 You can do this by adding "netcdf" to the end of your trajout statement.
 For example:

trajout A6WTnoWAT.mdcrd netcdf nobox

Hope this helps,

On Mon, Jan 10, 2011 at 5:52 PM, Daniel Scott <> wrote:

> Hi AMBER users,
> If I have a gzipped trajectory file, the following ptraj command writes a
> new trajectory file (.mdcrd) without the water:
> trajin A6WT_0_md_prod_1.mdcrd.gz
> strip :WAT
> trajout A6WTnoWAT.mdcrd nobox
> Can I then calculate other ptraj commands (i.e., "dihedral," "analyze
> timecorr," etc.) using these commands:
> trajin A6WTnoWAT.mdcrd
> vector D26CO .365 corr @366
> analyze timecorr vec1 D26CO tstep 200 tcorr 20000000.0 out D26COcorr.out
> so that the time correlation function calculations are a lot faster? You
> see, I have 100 of these .gz files, and it takes about 24hrs for a ptraj
> calculation to run. I'm trying to save time by writing a new trajectory
> file without the waters.
> Thanks for any advice,
> Daniel Scott
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jan 10 2011 - 16:00:04 PST
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