From: doty alexiou (doty_alexiou_at_hotmail.com)
Date: Wed Jul 14 2010 - 04:33:12 CDT
.right,i was wrong.I mean the parameter file.I was wondering how could i gather information from a specific AllAtom-Sim & add new lines in rbcg-2007.par file for the parameterization.Thank u.
Date: Wed, 14 Jul 2010 00:08:57 -0400
From: felmerino_at_uchile.cl
To: doty_alexiou_at_hotmail.com; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: RBCG
Hey,
Correct me if i am wrong, but i think when you say topology you actually mean the forcefield parameters.
Sure you can. You can obtain a probability distribution from an all atom simulation for any feature of a set of degrees of freedom. Then using the relationship p(x) = exp (-V(x)/kT), where V(x) is the potential you can obtain new ad hoc parameters.
take a look at the nanodisc papers where the parameters set that comes with VMD where obtained.
best
felipe
----Mensaje original----
De: doty_alexiou_at_hotmail.com
Fecha: 13-07-2010 03:42
Para: "namd-list"<namd-l_at_ks.uiuc.edu>
Asunto: namd-l: RBCG
Hello.If i am not wrong, u can add new information to your topology file using paratool on vmd and QuantumMechanical simulatios as a base.Is there a way to add new information to my CG topology file using all-atom simulations as a base?(i use the RBCG method)
thank u,Dota.
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