From: ipsita basu (ibasu788_at_gmail.com)
Date: Wed Feb 17 2010 - 23:09:16 CST
Actually I have the problem during minimization. I give 10000
minimisation in my input, but the job is aborted after doing few steps of
minimization . I can't reach to the md part at all. Please help me . How can
I find which patch is missing in psf file?
On 2/16/10, Jeffrey J. Potoff <jpotoff_at_chem1.eng.wayne.edu> wrote:
> To follow up on Axel's post, getting a bilayer system started can be
> somewhat difficult. We have found that CHARMM_GUI
> produces starting configurations for lipid bilayers that are reasonably
> well minimized/equilibrated such that one can initiate heating and dynamics
> without much effort.
> Your output also suggests that your PSF file might have some errors in it
> (missing patch).
> ipsita basu wrote:
>> 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
>> -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:
>>  [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
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
-- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009
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