From: Yogesh Aher (aher.yogesh_at_gmail.com)
Date: Mon Jul 13 2009 - 05:57:18 CDT
Dear NAMD- users!
I was trying to run simple namd run for my homology-modelled protein which
is quite big in size.
It's PBC dimensions are like this (after solvating with option -t 5):
# Periodic Boundary Conditions
cellBasisVector1 105. 0. 0.
cellBasisVector2 0. 121. 0.
cellBasisVector3 0. 0. 125.
cellOrigin 21. 73. 27.
PME GRID DIMENSIONS 108 128 128
But I get the following error:
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
I increased cutoff values along with the pairlist-distance, but no impact of
them on avoiding this error. (Is there any rule of thumb to calculate cutoff
values depending on the PBC and PME dimensions?)
I read other posts with the same subject, but couldn't get the relevant
solution, so thought to raise this question again.
Looking forward for your valuable suggestions..
Thanking you,
Y.
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