VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jun 30 2008 - 11:42:26 CDT

On Mon, 30 Jun 2008, S.K. Ghosh wrote:

SKG> Hi VMD users,
SKG>
SKG> I am trying to use namdstat.tcl script to find the change in Temp over
SKG> time. I am getting the below-mentioned errors. Could you please help me get
SKG> over this error.

this problem was discussed on the NAMD list just two weeks ago.

the parser in the namdstats.tcl script that locates the ENERGY:
output lines is very simple and assumes that you have only a
small number of time steps. please try the attached version.

axel.

SKG>
SKG> My logfile has 3million steps and Temp data is written every 100 steps i.e.
SKG> 30,000 data points.
SKG>
SKG> >Main< (4-7-bs-ws-nve) 24 % data_time TEMP bs_ws_nve.log first 3000000
SKG> Getting TEMP data...
SKG> can't read "e(10001,2)": no such element in array
SKG>
SKG> >Main< (4-7-bs-ws-nve) 26 % data_time TEMP bs_ws_nve.log 1000000 1999900
SKG> Getting TEMP data...
SKG> can't read "e(10001,2)": no such element in array
SKG>
SKG> Again, when I am doing the following, there's no eror but I am getting
SKG> results for 0th till 999,900 steps (10,000 data points).
SKG>
SKG> >Main< (4-7-bs-ws-nve) 25 % data_time TEMP bs_ws_nve.log
SKG> Getting TEMP data...
SKG> Done
SKG>
SKG> Your help would be much appreciated.
SKG>
SKG> Thanks,
SKG> Sourav
SKG>
SKG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.