Hi Marek,
If I understand your problem wright, I was thinking along the line of
radial CH1.RDF 0.1 50.0 :1-5 !(:1-5) noimage. Wouldn't that do the same thing for INTER-molecular RDF only?
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Marek Maly [marek.maly.ujep.cz]
Sent: Friday, November 23, 2012 3:13 PM
To: AMBER Mailing List
Subject: Re: [AMBER] INTER-molecular RDF only ?
Hi Mohd,
let's suppose that I have some molecules which are composed of residues,
STP,REP,ENP (in my case linear chain).
If I use common RDF command like:
radial Ch.RDF 0.1 50.0 :ENP,REP,STP :ENP,REP,STP noimage
I obtain the RDF where the intra-molecular distances distribution is
mixed with that inter-molecular but I would like to obtain only
inter-molecular part which contain just the information about the
distances between atoms from different molecules.
Finally I got the idea how to obtain it, simply to do also the same
analysis but just
with one molecule to obtain intra-RDF part like
radial Ch1.RDF 0.1 50.0 :1-5 :1-5 noimage
(if one of that molecules is composed of residues 1-5)
Of course using the same or longer part of trajectory used for the global
RDF (to analyze enough
of molecule conformations) and perhaps to do it also for several isolated
molecules not only for one, than to do RDF average which would represent
good estimate of intra-molecular part, this might be then substracted from
the above global RDF and I should have estimate of the inter-molecular RDF
part only.
But would be more comfortable to have some flag like INTER and if you use
it like here:
radial Ch.RDF 0.1 50.0 :ENP,REP,STP :ENP,REP,STP noimage INTER
it calculates only inter-molecular RDF, or the global one, inter-molecular
and intra-molecular
all together.
Can you please more in detail describe your solution ?
Thanks in advance !
Best wishes,
Marek
Dne Fri, 23 Nov 2012 21:34:31 +0100 Ismail, Mohd F. <farid.ou.edu>
napsal/-a:
> I don't get it. What's the difference between such an implementation
> versus just using a different mask?
>
> *******************************
> Mohd Farid Ismail
> Graduate Student
> Dept. of Chemistry/Biochemistry
> University of Oklahoma
> Norman 73019
>
> ________________________________________
> From: Marek Maly [marek.maly.ujep.cz]
> Sent: Friday, November 23, 2012 7:22 AM
> To: amber.ambermd.org
> Subject: [AMBER] INTER-molecular RDF only ?
>
> Hello all,
>
> I am just wondering if there is any possibility to calculate
> only inter-molecular radial distribution function using AmberTools12
> i.e. not taking in account atoms distances which are within the given
> molecules
> (elements with covalent bond connectivity) but only distances between
> atoms
> belonging to different molecules.
>
> If not, I would suggest to include this possibility in some future
> AmberTools version,
> as it might be very valuable feature in applications where the study of
> molecular distribution
> within the given system (depending on different adjustable parameters)
> is
> the important
> information/characteristic. In case of small molecules it is not a big
> problem as one can represent
> such molecule with one specific atom, but in case of bigger molecules
> (moreover flexible like
> some chains) such trick might be insufficient.
>
> Thanks for eventual comments/suggestions !
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
>
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Received on Fri Nov 23 2012 - 14:30:02 PST
