MMTSB Tool Set for CHARMM/NAMD generated trajectory DCD files

[slaw]

Xiang-Jun,

I just wanted to add that for simulations generated from CHARMM/NAMD that produce trajectory files in a binary format (sometimes named "DCD" files), one could use the MMTSB Tool Set:

http://blue11.bch.msu.edu/mmtsb/Main_Page

Click "Download" in the menu.

Although the MMTSB Tool Set was created in an effort to make simulating in CHARMM much easier, there is a script called "processDCD.pl" that, if used in the right way, can be used in conjunction with 3DNA (I've done this myself):

http://blue11.bch.msu.edu/mmtsb/processDCD.pl

I would be happy to share my experiences with using the MMTSB Tool Set.

Sean

[xiangjun]

Hi Sean,

Thanks for sharing the info -- I came across MMTSB before, but did not get a chance to play with it. This is the first time I hear of the binary DCD trajectory files produced by CHARMM/NAMD. The Perl script "processDCD.pl" seems useful, too. I've downloaded MMTSB, and would like to spend some time to it.

I would be happy to share my experiences with using the MMTSB Tool Set.

That would be great! In addition to Alpay's Python script (which I have moved to this section), my Ruby scripts, now users will have access to a Perl version of analyzing MD trajectories using 3DNA! Please start a new thread in this  "Molecular dynamics simulations" section; and remember to provide a concrete example so that others can follow. I'd also be interested in seeing an sample DCD file.

Best regards,

Xiang-Jun