analysis of dcd

From: ipsita basu (ibasu788_at_gmail.com)
Date: Sun Jan 31 2010 - 22:58:41 CST

Dear all,
            I have run a very short simulation of 500 ps. In the input dcd
freq was 2500 and the total step is 250000 and time step 2 fs ( tot 500 ps
). Now I want to convert the dcd to crd for the final step to see the final
situation. That's why the output.dcd was read in charmm and the command was
:
coor dyna firstu 51 nunit 1 begin 250000 stop 250000 .
But the log file gives error like :
 READING TRAJECTORY FROM UNIT 51
   NUMBER OF COORDINATE SETS IN FILE: 100
   NUMBER OF PREVIOUS DYNAMICS STEPS: 2500
   FREQUENCY FOR SAVING COORDINATES: 2500
   NUMBER OF STEPS FOR CREATION RUN: 250000

 ***** ERROR ***** NO. OF ATOMS DO NOT MATCH 29566 27334
 *** LEVEL -4 WARNING *** BOMLEV IS 0
 BOMLEV HAS BEEN SATISFIED. TERMINATING.
But if I change the begin step to 2500 and stop also 2500, then there is no
problem.
 So what should I do to solve the problem? Please help me.

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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