AMBER Archive (2009)

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

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Thu Feb 19 2009 - 10:39:15 CST

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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