From: Harish Vashisth (harish.vashisth_at_gmail.com)
Date: Tue Jul 22 2014 - 11:23:13 CDT
We have been trying to make use of many CVs (> 20) using abf/colvar
options in NAMD2.9. These are all backbone dihedral CVs defined
individually in multiple blocks of phi/psi, etc. We are able to run ABF
jobs fine up to 5 CVs, but including a sixth one or more does not work. The
error reported in the log file right after initialization of colvars module
FATAL ERROR: Memory allocation failed on processor 0.
Looking through previous posts, someone seemed to suggest that it is likely
occurring due to large system size as NAMD keeps a copy of the system on
In our case, the solvated system size is ~40,000 atoms. The error occurs
using NAMD2.9 on local workstation, our local CRAYXE6m-200 as well as on
Stampede (XSEDE resource.) Is there an upper limit on how many CVs colvar
module can handle?
Any suggestions would be helpful. Thanks.
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