From: ipsita basu (ibasu788_at_gmail.com)
Date: Tue Feb 16 2010 - 05:26:07 CST
Dear all,
I have prepared a bilyer in charmm and make psf file in
xplor format. I want to minimise and then equilibrate it in namd. But
the job is aborted. My input is attached here and some of the errors
are given below:
ERROR: Stray PME grid charges detected: 1 sending to 3 for planes 97 98 99
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global dihedral count!
Warning: Stray PME grid charges ignored!
PRESSURE: 2321 1.74905e+10 -2.63334e+09 -1.65952e+10 -2.63334e+09
4.97756e+08 2.54818e+09 -1.65952e+10 2.54818e+09 1.58308e+10
GPRESSURE: 2321 1.74926e+10 -2.63287e+09 -1.65934e+10 -2.63338e+09
4.98307e+08 2.54861e+09 -1.65959e+10 2.54445e+09 1.58289e+10
ENERGY: 2321 58066783.1514 6197301.7556 5003.8692 331.3541
-93129.8653 99999999.9999 0.0000 0.0000 0.0000
99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000
99999999.9999 99999999.9999 799507.5942 99999999.9999 99999999.9999
ERROR: Stray PME grid charges detected: 0 sending to 2 for planes 50
51 54 55 56 57
ERROR: Stray PME grid charges detected: 1 sending to 3 for planes 79
80 81 82 83 84 85 86 87 88 89 90 91 92 93
Warning: Tuple 5033 with atoms 5063(23) 5066(41) missing patch 41
FATAL ERROR: Patch needed for tuple is missing.
Stack Traceback:
[0] [0x8246780]
Can you please suggest me what is the solution of it? I read such
problems in namd-mailing list and according to some thread I increase
pmegridsize. But doing this the job is running for few steps more but
aborted finally. Please give me some suggestions.
Thanking You
Ipsita Basu
-- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009
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