Not sure if someone pinged you. I have used this nfe module before (on a toy system). it is located in around here : /src/pmemd/src/nfe_stsm.F90
I used the toy system from the neb tutorial: http://ambermd.org/tutorials/advanced/tutorial5_amber11/section3.htm to make sure I was performing it correctly. You should make a groupfile and each image should be labeled as ${image}.eq.0
-O -p ./str1.prmtop -c ./1.eq.0 -i swarm1.mdin -x ./swarm1.x.000 -o ./swarm.out.000 -inf ./swarm.info.000 -r ./swarm.r.000
-O -p ./str1.prmtop -c ./2.eq.0 -i swarm2.mdin -x ./swarm2.x.001 -o ./swarm.out.001 -inf ./swarm.info.001 -r ./swarm.001
etc...
you can rename the neb.r.${number} to follow the format.
Amber Advanced Workshop - Tutorial 5 - Nudged Elastic Band - Section 3: Creating the NEB prmtop and inpcrd files<http://ambermd.org/tutorials/advanced/tutorial5_amber11/section3.htm>
A tutorial on how to use the new Nudged Elastic Band (NEB) implementation that is part of the Amber 9 Molecular Dynamics Software. Finding a low energy pathway for alanine dipeptide isomerization. Section 3: Creating the NEB prmtop and inpcrd files
ambermd.org
________________________________
From: Souvik Dey via AMBER <amber.ambermd.org>
Sent: Thursday, March 23, 2023 11:09 AM
To: David A Case <david.case.rutgers.edu>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Implementing string method in AMBER
Thank you for the response. Yes, I am already familiar with section 25.4.6
of the manual and the tutorial 7.12. At this point, my main area of
confusion is how to specify the images in the input files. I want to run
the sequential version as shown in Figure 25.16 but unsure of how to
interpret the image=I command. Should I name my PDBs as 0.pdb, 1.pdb and so
on?
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Received on Sat Mar 25 2023 - 18:00:03 PDT
