On Sat, Jan 7, 2012 at 12:47 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
> Thank you , Dr. David.
>
Now, I am trying to calculate time-correlation functions of C-H vecors
of methyl sidechain of leucine [it has two methyl groups] using ptraj.
Please help me.
[ in
http://archive.ambermd.org/201005/0071.html, I understand that vectors
are given for N-H vector of backbone, e.g vector v2 :2.N corr :2.H ]
Thanks,
Mahendra Thapa
>
> ________________________________________
> From: David A. Case
> Sent: Saturday, January 07, 2012 11:46:56 AM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] calculation of spectral density
>
> On Thu, Jan 05, 2012, Mahendra B Thapa wrote:
>
> > I got the output files after 50 nS molecular dynamics
> > simulation of a protein using AMBER 11. Let me help how to process these
> > data to get spectral density to get plot of J(0) and residue number.
>
> You need to state which "spectral density" you are interested in.
> Generally,
> Amber supports calcualtion of time-correlation functions (see the ptraj
> section of the manual). J(0) is just the area under the C(t) curve, but
> you
> would have to calculate that yourself (either by numerical intergration,
> or by
> fitting C(t) to some analytic function, the integrating the latter.)
>
> ...good luck....dac
>
>
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>
>
>
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Received on Thu Feb 16 2012 - 12:30:02 PST
