From: Pang, Yui Tik (andrewpang_at_gatech.edu)
Date: Thu Nov 12 2020 - 15:25:58 CST
Dear Peter,
I am the co-developer of GaMD and am happy to answer your question. The boost potential was applied on the source code level which involves modifying the "Controller" module of NAMD. You may grep "accelMD" from the NAMD source code to find out the details.
It is, however, usually not necessary to modify NAMD source code to add customize bias potential. There are several ways to do it, like scriptedFunction in colvars, TclForce or TclBC. You may explore different approaches before going down the path of modifying NAMD source code.
Hope it helps.
Best,
Andrew
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Peter Rosenquist <per20_at_georgetown.edu>
Sent: Thursday, November 12, 2020 4:00 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Adding bias potential
Hello,
I am trying to add a custom bias potential along the lines of aMD or GaMD, specifically the /delta*V(r) of: V*(r) = V(r) + /delta*V(r), where V(r) is original potential and /delta*V(r) is defined as the output of my custom function p(r). How does aMD add the bias potential? Is there another way to do this in NAMD?
Best,
Peter
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