VMD-L Mailing List

From: Joe Huang (HCHuang_at_uh.edu)
Date: Thu Mar 20 2003 - 13:02:48 CST

Dear VMD users,
I am running a kind of RMSD comparisons (segment by segment on Protein
or RNA) with TCL script under VMD1.8.
The system is huge and the calculations can be ~ (1500 X 1500) RMSD
calculations (i.e., 2.25 E6 or more than 2 million RMSD calculations).
 In the beginning, my calculations would crash due to the consumptions
of virtual SWAP memory in the system after ~ 4 rounds of RMSD
calculations (i.e., ~[4x1500] out of more than 2 million calculations);
later, I checked the VMD-L archive and found out that I need to unset
the atom selections after each RMSD comparison to solve this problem.
 Therefore, I unset the atomselections (e.g., "unset
upproc_var_$compare" and "unset upproc_var_$reference") and also unset
all the variables (e.g., "unset trans_mat", "unset rmsd", ...etc.)
after their usages on each cycle; in this case, the calculations could
go on more than (400x1500) comparisons, but the virtual SWAP memory was
still decreasing in a much slower slower degree and eventually the
calculations would still crash in the middle to the finish line!
 Although I could rerun VMD and recontinue the job several times to
finish the whole calculations, I prefer to finish it just by one session
of VMD calculations with TCL script. So, does anyone know what causes
the calculations to slowly consume the SWAP memory and also know the
solution to it?
Your help will be much appreciated!!

Joe 

-- 
 *****************************************
 Hung-Chung Huang, M. T., M. Sc., Ph. D.
 Department of Biology and Biochemistry
 University of Houston, Houston, TX 77204
 Tel: (713) 743-8365, Fax: (713) 743-8351
 e-mail: HCHuang_at_uh.edu
 http://prion.bchs.uh.edu/~jhuang
 *****************************************