Hi Dan
I see, thank you for clarification. I tried your suggestion and I get some invalid command error messages:
[trajin MD333.mdcrd]
Reading 'MD333.mdcrd' as Amber Trajectory
[for residues R0 in mask :FSI i=1;i++]
Error: Unrecognized character in expression: :
'for residues R0 in mask :FSI i=1;i++': Invalid command or expression.
1 errors encountered reading input.
Do you see where the problem lies?
Thanks for your help,
David
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Donnerstag, 30. Mai 2019 17:03
> To: AMBER Mailing List
> Subject: Re: [AMBER] Radgyr or distance averages
>
> Hi,
>
> On Wed, May 29, 2019 at 11:24 PM Reber, David <David.Reber.empa.ch>
> wrote:
> > If I calculate the radius of gyration or atom-atom distances for one
> particular molecule in my trajectory I obtain values I would expect.
> > e.g. my 9-atom anion called FSI(resid 1) "radgyr :1 out ***.dat mass
> tensor" yields something like 1.9 Angstrom.
> > If I select all the molecules of a certain type I get values that are
> approximately half the box size:
> > "radgyr :FSI out ***.dat mass tensor" yields ca. 20 Angstrom.
>
> So as you are seeing, by default the atom masks in these commands
> apply to all atoms. That is, something like :WAT for 'radgyr' will
> calculate the radius of gyration of *all* water molecules in your
> system. So what you would need to do is create a loop over whatever
> molecules/residues, then calculate the average. So something like this
> should work:
>
> parm myparm.parm7
> trajin mytraj.nc
> for residues R0 inmask :FSI i=1;i++
> radgyr rg$i $R0
> done
> avg oversets rg* name AvgRg out AvgRg.dat
> run
>
> If you want the individual radius of gyration values for each residue,
> just add 'out rg.dat' or something to the 'radgyr' command. Hope this
> helps,
>
> -Dan
>
>
> >
> > I have the same issue with the distance command. If I select two atoms on
> resid 1 I get reasonable values in the range of 3-4 Angstrom:
> > "distance :1.F1 :1.F2 out distance.dat"
> >
> > if I select all FSI-residues, I get values of about 0.2 A:
> > "distance :FSI.F1 :FSI.F2 out distance.dat"
> >
> > In case of the distance command I assume intermolecular distances are also
> calculated which in the end cancel each other out resulting in the value close
> to zero?
> >
> > How can I get the average radgyr or intramolecular atom-atom distances
> for a certain type of molecule averaged over the whole trajectory?
> >
> > Thank you in advance for any hints,
> >
> > David
> >
> >
> >
> >
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>
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Received on Thu May 30 2019 - 18:00:02 PDT
