AMBER Archive (2009)

Subject: [AMBER] RE: suggestions

From: Ross Walker (
Date: Mon Jul 06 2009 - 20:01:51 CDT

Hi Raja,

Please post such questions to the AMBER mailing list, where I am cc'ing
this. See for signup details.

You can accomplish what you want do by providing ptraj with a set of ranges
for the trajin command. E.g. if you were writing to the trajectory file once
every 1 ps, then for 12 ns you would have 12000 frames in your trajectory.
Thus in ptraj you would specify:

trajin foo.mdcrd 2001 12000 1

To read every frame between 2001 (2.001ns) and 12000 (12ns).

All the best


From: Raja Pandian []
Sent: Monday, July 06, 2009 11:01 AM
Subject: suggestions


Respected Sir,

I need some suggestions for you.

#I have 12ns trajectory. Now I want to split that into two parts, up to 2ns
will be an equilibration period and then the remaining 10ns as mine
production time. For this, how I can write the ptraj ( file?
Because I want to do analysis on this production (10ns) time. How to
remove/neglect the initial 2ns from mine 12ns trajectory?

Here I have attached mine file.

#I would like to do the Dynamic Cross Correlation Map (DCCM) analysis.
Searching AMBER archive showed that similar questions have been posted
before but no answer. If it is possible, please send me the brief
explanation about DCCM analysis and how to do that one?

Thanks in advance for your suggestions.





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