Re: dump specific atom positions into a txt file during the simulation

From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Fri Aug 31 2012 - 03:15:56 CDT

Hi Ehsan, I need to extract the positions much more frequently than what it is in the dcd file (I would rather to don't generate huge dcd files...). Therefore, I want to know if I can do this by adding a couple commands in the config file thanks, jackie ________________________________ From: Ehsan Ban <ehsan.ban_at_gmail.com> To: Jacqueline Schmidt <jacqueline_schmidt_1983_at_yahoo.com> Sent: Friday, August 31, 2012 4:08 AM Subject: Re: namd-l: dump specific atom positions into a txt file during the simulation Dear Jackie, 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 I wish this is helpful. Best Regards Ehsan On Fri, Aug 31, 2012 at 2:14 AM, Jacqueline Schmidt <jacqueline_schmidt_1983_at_yahoo.com> wrote: Dear Namd users, >How can I dump the postitions of specific atoms into a file (I want this more frequently than the movie files)? So I guess there should be a way to define a group including my atom of interests and then dump their positions into a text file... >Can anyone help please? >Many thanks >jackie

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