VMD-L Mailing List

From: Alexander Balaeff (abalaeff_at_gmail.com)
Date: Fri Jan 27 2017 - 00:03:15 CST

Dear VMD community:

Could anyone possibly suggest a workaround of VMD running out of
memory due to (suspected) multiple file opening? In the attached
script, I am repeatedly reading frames from a DCD file(*) using mol
addfile; basically, with this sequence repeated in two nested loops:

    animate delete all 0
    mol addfile $dcd_file(0) first $i last $i waitfor all 0

End result: VMD (LINUXAMD64 version 1.9.2beta1) runs out of memory. I
see nothing else in the script that could cause it and suspect the
issue is VMD running afoul of the TcL file handling: opening the same
file multiple times, growing some intrinsic buffers for file reading,
etc., etc.

Has anyone encountered similar issues? Would using animate read
instead of mol addfile work better? Any suggestion would be greatly
appreciated.

Best,

Alexander.

(*) The reason I am doing so is that the whole DCD file wouldn't fit
to the memory and I want to avoid reading it by pieces and then
stitching the results together.

=====================================================

Prof. Alexander Balaeff

 University of Central Florida
 NanoScience Technology Center
 12424 Research Parkway, Suite 400
 Orlando, FL 32826

 Phone: (407) 823-4576
 FAX: (407) 882-2819
 E-mail: abalaeff_at_gmail.com