AMBER: Questions/observations about Nudged Elastic Band (NEB)

From: Pietro Amodeo <>
Date: Thu, 28 Sep 2006 12:56:36 +0200 (CEST)

Dear Amber users,

1) after a careful reading of both AMBER9 manuals and Ross Walker's
Tutorial 7 from "Amber Workshop Tutorials" I understood that NEB approach
can be performed using multiple frames from an approximate path as
starting guess for min. energy paths. In the case of our simulated
molecule, we obtained the desired conformational transition during a
standard MD simulation using implicit GB/SA solvation. Now, we'd like to
obtain a NEB path using frames from this MD simulation. What MD protocol
(in particular, temperature vs. time profile and frequency of frame
sampling from original MD run) is suggested in this case?

2) looking at the source code of AMBER9 implementation of the quenched
velocity Verlet algorithm used for NEB minimization (see below), we
observed that, differently from what stated in the manual, when the dot
product v dot f<0 , velocities are simply zeroed and not scaled according
to eq. (6.34) v=x(v dot f)f and, consequently, the input scaling factor
VFACT is never used (or, equivalently, the program behaves as if VFACT
value were hardwired to 0). I've found no explanation for this discrepance
either in docs, or in man. upgrades, or in mailing list, or in bugfixes.

>>>> File: runmd.f
>>>> Subroutine: quench
> if (dotproduct>0.0d0) then
> v(1:3*natom) = dotproduct*f(1:3*natom)*force
> else
> v(1:3*natom) = 0.0d0
> end if

Thank you in advance for any answer or explanation,

Dr. Pietro Amodeo
Istituto di Chimica Biomolecolare del CNR
Comprensorio "A. Olivetti", Edificio 70
Via Campi Flegrei 34
I-80078 Pozzuoli (Napoli) - Italy
Phone      +39-0818675072
Fax        +39-0818041770
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Received on Sun Oct 01 2006 - 06:07:11 PDT
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