[gmx-developers] [Fwd: your kind advice needed]

Berk Hess hessb at mpip-mainz.mpg.de
Thu Mar 2 09:04:24 CET 2006

-------- Original Message --------
Subject: 	your kind advice needed
Date: 	Wed, 1 Mar 2006 21:47:25 +0000
From: 	Marie <ma7 at soton.ac.uk>
To: 	hessb at mpip-mainz.mpg.de

 Dear Sir

I am intending to implement Hybrid Monte Carlo in Gromacs which simply
collects energies (kinetic and potential) and accepts/rejects new
coordinates based on total (kinetic + potential) energy using Monte Carlo
test. If the new positions are failed, the old positions are restored and
the momenta is regenerated randomly using gaussian distribution.

My question is how easy would it be for me to get into the Gromacs code. I
am not worried about the coding but about the dead ends where its not
possible to implement such scheme into one integrator (HMC) and call MD
integrator within it to make MD moves and perform what I described above. I
have had bad experience with NAMD as its doesnt allow abstraction and
flexibilty the way its integrator works so before I start my work on
Gromacs, I would be really grateful to you for your kind advice.

Many thanks for your time


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