AMBER Archive (2009)

Subject: Re: [AMBER] dipole correlation function

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Feb 19 2009 - 08:39:16 CST


I don't think you want to use imaging if you are calculating
correlation functions. however, I really don't udnerstand your ptraj
script- are you trying to overlap all of the waters? I don't think
this would ever do anything useful once the waters move around. also,
won't the overlap change the correlation?

On Thu, Feb 19, 2009 at 9:18 AM, Jeffrey <jeffry20072008_at_yahoo.cn> wrote:
> 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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> http://cn.mail.yahoo.com
>
>
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