AMBER Archive (2009)

Subject: [AMBER] dipole correlation function

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Thu Feb 19 2009 - 08:18:20 CST

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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