From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Sun Sep 09 2007 - 07:37:50 CDT
Hi,
I have a large POPC bilayer (110 x 110 A) hydrated and built using membrane
and then solvated using solvate.tcl. When I run minimization, I get an
error:
###############
Warning: Tuple 73108 with atoms 38265(68) 38268(118) 38271(27) missing patch
118
ERROR: Stray PME grid charges detected: 24 sending to 8 for planes 29 30 31
ERROR: Stray PME grid charges detected: 24 sending to 10 for planes 36 37 38
39
ERROR: Stray PME grid charges detected: 24 sending to 5 for planes 19
ERROR: Stray PME grid charges detected: 24 sending to 6 for planes 20 21 22
ERROR: Stray PME grid charges detected: 24 sending to 9 for planes 32
ERROR: Stray PME grid charges detected: 26 sending to 5 for planes 16 17 18
19
ERROR: Stray PME grid charges detected: 26 sending to 8 for planes 28
ERROR: Stray PME grid charges detected: 23 sending to 5 for planes 16
ERROR: Stray PME grid charges detected: 23 sending to 4 for planes 12 13 14
15
FATAL ERROR: Patch needed for tuple is missing.
#################
A look at the trajectory in vmd (3 frames, saved every 5000 steps) shows
several bonds highly extended and reaching out of the main simulation box.
The lines starting with ERROR start appearing after about 40-50 steps of
minimization, and the simulation crashes after about 15000 steps of
minimization.
My PME grid is 120 x 120 x 180. The simulation box size is 113 x 114 x 171
The number of atoms is about 220,000. I am running on 8 nodes, each of which
is 4 cpus.
The bilayer is asymmetric in the sense that one layer of hydrating water
(100 A) is much thicker than the other (30 A).
Any suggestions what might be happening ?
Thanks !
-Maria
-- Maria G. Technical University of Denmark Copenhagen
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