Hi,
Are you really interested to see the fluctuations of water molecules within the system?
If you only interested to calculate the residue wise fluctuations, then may be this mask (@N,CA,C for proteins or maybe :1-end_residue_number) would suffice your need.
You may try this script:
Parm *.prmtop
Trajin *.nc
Rms first
Average MyAvg.pdb pdb
Run
Reference MyAvg.pdb
Rms reference @N,CA,C
Atomicfluct .N,CA,C out fluct.dat byres
Run
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________________________________
From: Roy, Rajarshi <roy212.purdue.edu>
Sent: Monday, April 24, 2023 10:44:35 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Query regarding atomicfluct command
Hi,
This is the total number of atoms in my system including the water.
Sincerest thanks
Rajarshi Roy
Post Doc Research Associate
Purdue University
________________________________
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Sent: Monday, April 24, 2023 12:51 PM
To: Roy, Rajarshi <roy212.purdue.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Query regarding atomicfluct command
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Hi,
Does your system contain 227775 molecules or is it including water also?
Satyajit
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From: Roy, Rajarshi via AMBER <amber.ambermd.org>
Sent: Monday, April 24, 2023 10:11:57 PM
To: Roy, Rajarshi via AMBER <amber.ambermd.org>
Subject: [AMBER] Query regarding atomicfluct command
Dear AMBER users and developers,
I require assistance with the "atomicfluct" command in Amber. Despite using the command snippets provided in the manual, I encountered an error message.
[rms ref MyAvg]
TIME: Total execution time: 10.7006 seconds.
Error: Reference mode # atoms on rank (0) != # atoms on master (227775)
Error: Could not initialize action [rms]
1 errors encountered reading input.
Error: Error(s) occurred during execution.
The reason for receiving this could be unclear as there is only one reference provided here.
Code snippet used here (Using same as mentioned in the manual):
rms first
average crdset MyAvg
run
rms ref MyAvg
atomicfluct out fluct.dat
I would greatly appreciate any guidance or suggestions on how to resolve this issue.
Thank you in advance for your help.
Sincerest thanks
Rajarshi Roy
Post Doc Research Associate
Purdue University
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Received on Mon Apr 24 2023 - 10:30:02 PDT
