[gmx-users] Re: rotational correlation function

[Vitaly Chaban]

Hmm... Rotational time..? If you need diffusion constant, just use
g_rotacf and then integrate the resulting VACF. If I recall correctly,
you should make an index file with three numbers to define two vectors
for the calculation.


On Wed, Sep 22, 2010 at 7:27 PM, Paymon Pirzadeh <ppirzade at ucalgary.ca> wrote:
> Dear Dr. Chaban,
> I meant the N-H bond vectors of protein backbone for calculation of
> rotational time correlation function to calculate the rotational
> diffusion constant of my protein. I need a protocol which walks me step
> by step through the procedure.
> Thanks for your Attention.
>
> Paymon
>
>
> On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
>> > Message: 2
>> > Date: Wed, 22 Sep 2010 12:07:27 -0600
>> > From: Paymon Pirzadeh <ppirzade at ucalgary.ca>
>> > Subject: [gmx-users] rotational correlation function
>> > To: gmx-users at gromacs.org
>> > Message-ID: <1285178847.11669.66.camel at paymon-desktop>
>> > Content-Type: text/plain
>> >
>> > Hello,
>> > Imagine if the total correlation function of a protein could be
>> > factorized into rotational and internal portions:
>> > Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
>> > and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
>> > What does the g_rms -fit do? I am confused on how I can use gromacs
>> > commands on my output files. Sorry for mass of e-mails.
>> >
>> > Paymon
>>
>>
>> Hey, Paymon -
>>
>> Do you mean the correlation function of the velocity (VACF)? Why not
>> to use g_velacc and g_rotacf for translational and rotational VACFs? I
>> suppose, your molecule is rigid (enough) for rotational velocoty to
>> make sense.
>>
>> --
>> Dr. Vitaly V. Chaban
>> Department of Chemistry
>> University of Rochester
>> Rochester, NY 14627-0216
>> United States of America
>
>