AMBER Archive (2009)

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

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Thu Feb 19 2009 - 19:31:08 CST

Hi Carlos, I used this script to calculate dipole values of each frame in the trajectory. Then dipole correlation will be calculated basing on these dipole values. I know that RMS command would translate and rotate the frame to fit the reference structure, but don't know how it would affect the final correlation values when writing it in the script.

Another question:
NPT (ntt=3) simulation was carried out to equilibrate the water box for 1ns at the equilibrationg phase after the NVT heating process. At production phase, NVE was used to generate the trajectory. But some waters flied out from the primary box at the end of 1-ns NPT equilibration. Do you think the iwarap=1 should be added when using NPT equilibration? (sorry that I made a mistake in my first post where the iwrap=1 was used in the NVE ensemble. In fact my confusion is whether it should be used in NPT to keep a regular water box shape at the end of NPT equilibration for the starting structure of NVE production).

Thanks very much for the time.

-----
Jeffrey

>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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>>>>
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