AMBER Archive (2009)

Subject: Re: Re: [AMBER] dipole correlation function

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Feb 19 2009 - 11:23:03 CST

yes your ptraj script uses an rms command. make sure you know what it
is doing- it does not look helpful to me. did you make it yourself, or
get an example from someone for calculating the dipole correlation? I
would make sure that you are very comfortable with the more basic
options in ptraj before doing correlations.

On Thu, Feb 19, 2009 at 11:39 AM, Jeffrey <jeffry20072008_at_yahoo.cn> wrote:
> Hi Carlos, sorry that this is the first time I use ptraj module and some questions may be so simple. Do you mean that the RMS command is used in the ptraj script?
>
> Thanks very much.
>
> ---
> Jeffrey
>
>>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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>>
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