From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Fri Aug 31 2012 - 07:33:40 CDT
thanks tcl forces were so useful
jackie
________________________________
From: Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
To: Jacqueline Schmidt <jacqueline_schmidt_1983_at_yahoo.com>
Cc: Ehsan Ban <ehsan.ban_at_gmail.com>; namd <namd-l_at_ks.uiuc.edu>
Sent: Friday, August 31, 2012 4:44 AM
Subject: Re: namd-l: dump specific atom positions into a txt file during the simulation
>
>You have access to atomic coordinates and you can also write to files through Tcl Forces interface:
>http://www.ks.uiuc.edu/Research/namd/2.7/ug/node44.html
>
>
>or the Tcl Boundary interface:
>http://www.ks.uiuc.edu/Research/namd/2.7/ug/node45.html
>
>
That's a good idea!
What I have also done in the past is use the distance colvar with a dummy atom at the origin (as the ref group).
Another option is to run your simulations in shorter parts, pick the desired atoms from the dcd using VMD or catDCD and delete the original large dcd.
Best regards,
Ajasja
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