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From: Reber, David <David.Reber.empa.ch>

Date: Thu, 30 May 2019 03:24:20 +0000

Hello

I am using Amber16 and have the following question: How can I get the average radgyr or intramolecular atom-atom distances for a certain type of molecule averaged over the whole trajectory?

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.

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 Wed May 29 2019 - 20:30:02 PDT

Date: Thu, 30 May 2019 03:24:20 +0000

Hello

I am using Amber16 and have the following question: How can I get the average radgyr or intramolecular atom-atom distances for a certain type of molecule averaged over the whole trajectory?

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.

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed May 29 2019 - 20:30:02 PDT

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