Hi,
I have just tested it for my case. The script works perfectly for me. I am attaching for your reference:
Parm *.prmtop
Trajin *.nc
Rms first
Average crdset MyAvg
Run
Rms .N,CA,C ref MyAvg
Atomicfluct .N,CA,C out fluct.dat byres
Run
Best,
Satyajit Khatua
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________________________________
From: Roy, Rajarshi <roy212.purdue.edu>
Sent: Monday, April 24, 2023 11:45:20 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Query regarding atomicfluct command
Thanks for your help. However, I am getting the same error after incorporating your suggestions.
Sincerest thanks
Rajarshi Roy
Post Doc Research Associate
Purdue University
________________________________
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Sent: Monday, April 24, 2023 2:06 PM
To: Roy, Rajarshi <roy212.purdue.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Query regarding atomicfluct command
---- External Email: Use caution with attachments, links, or sharing data ----
Hi,
Try the script by updating only the
4th line as "rms .N,CA,C ref MyAvg" and see if it prints the same problem.
rms first
average crdset MyAvg
run
rms ref MyAvg
atomicfluct .N,CA,C out fluct.dat byres
Best,
Satyajit Khatua
Get Outlook for Android<
https://aka.ms/AAb9ysg>
________________________________
From: Roy, Rajarshi <roy212.purdue.edu>
Sent: Monday, April 24, 2023 11:27:40 PM
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Query regarding atomicfluct command
Hi,
Thank you for your prompt response. I had a command to compute the rmsf that was similar to that you posted. Nevertheless, I decided to try out the commands provided in the manual as an example and encountered an error. I'm unsure of the reason for this error. Therefore, I have reposted the code for your convenience.
rms first
average crdset MyAvg
run
rms ref MyAvg
atomicfluct @N,CA,C out fluct.dat byres
Sincerest thanks
Rajarshi Roy
Post Doc Research Associate
Purdue University
________________________________
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Sent: Monday, April 24, 2023 1:28 PM
To: Roy, Rajarshi <roy212.purdue.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Query regarding atomicfluct command
---- External Email: Use caution with attachments, links, or sharing data ----
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
---- External Email: Use caution with attachments, links, or sharing data ----
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 - 11:30:02 PDT
