[AMBER] dipole correlation function

From: Jeffrey <jeffry20072008.yahoo.cn>
Date: Thu, 19 Feb 2009 22:18:20 +0800

Dear all,

   We want to extract the dipole of a water box and then calculate the dipole correlation function. The trajectory was generated by the following two scripts:
----- 1
NVE production
&cntrl
   imin=0,
   ntx=5, irest=1,
   ntpr=100, ntwx=1000,ntwr=5000,
   dt=0.001,nstlim=1000000, nscm=5000,
   cut=9.,dielc=1.0,
   ntb=1,
   ntt=0,
   ioutfm=1
/

----
====2
NVE production
&cntrl
   imin=0,
   ntx=5, irest=1,
   ntpr=100, ntwx=1000,ntwr=5000,
   dt=0.001,nstlim=1000000, nscm=5000,        
   cut=9.,dielc=1.0,                                         
   ntb=1,                                   
   ntt=0, 
   ioutfm=1,
   iwrap=1
/
======
The calculated dipole values were not the same from two trajectories produced by above two scripts from the same starting structure,respectively. 
Which one should we use?
The dipole script:
*******
trajin npt1.dcd 1 1000 1
trajout merge.dcd
rms first out rms.dat .O,H1,H2
vector dip :WAT dipole out dip.dat
*******
Many thanks.
-------
Jeffrey
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Received on Fri Feb 20 2009 - 01:17:59 PST