Re: [AMBER] Radgyr or distance averages

From: Daniel Roe <>
Date: Thu, 30 May 2019 11:03:21 -0400


On Wed, May 29, 2019 at 11:24 PM Reber, David <> 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
for residues R0 inmask :FSI i=1;i++
  radgyr rg$i $R0
avg oversets rg* name AvgRg out AvgRg.dat

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


> 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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Received on Thu May 30 2019 - 08:30:02 PDT
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