Not precisely because,
#1
In the system I have several types of molecules and in the given
moment I would like to have inter-molecular RDF of just let say molecule
X=ENP+3xREP + STP.
But of course in that case I just set properly the second mask ( now
!(:1-5) )
to contain just molecules X different from :1-5.
#2
but even then your algorithm will in my opinion not reconstruct the true
inter-molecular RDF part as this should be based on doing radial density
analysis of each molecule X with respect to all remaining molecules X. Not
based just on density analysis of one "fixed" molecule X (e.g. 1-5),
with the respect to all remaining molecules. However in well homogenous
systems (without any clusters) might be perhaps this version:
radial CH1.RDF 0.1 50.0 !(:1-5) :1-5 noimage.
used for some inter-molecular estimate (with molecule :1-5 rather
somewhere in the center of the box).
Anyway thanks for your comment !
Best wishes,
Marek
Dne Fri, 23 Nov 2012 23:09:58 +0100 Ismail, Mohd F. <farid.ou.edu>
napsal/-a:
> 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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>
>
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