From: Victor Ovchinnikov (ovchinnv_at_gmx.com)
Date: Thu Jul 25 2013 - 12:56:52 CDT
Pedro,
This part of the NAMD code is obsolescent, which is probably why you
can't find the documentation for it.
Look at an old version of the UG (
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node34.html ) if you must
use it, or try something newer with similar functionality, such as the
colvars module or plumed (requires recompilation).
--Victor
On 07/25/2013 01:35 PM, Pedro Swagger wrote:
> Dear Experts,
>
> Sorry probably the way I asked were not the appropiate one. Could you
> please help me understand the command PMF in the following?
> What does task, time represents?
>
> Thanks so much
>
> pmf {
> task = grow
> time = 10 ps
> }
> pmf {
> task = up
> time = 200 ps
> print = 1 ps
> }
> pmf {
> task = stop
> time = 10 ps
> }
> pmf {
> task = down
> time = 200 ps
> print = 1 ps
> }
>
>
> On Wed, Jul 24, 2013 at 4:30 PM, Pedro Swagger
> <pedrito.swagger_at_gmail.com <mailto:pedrito.swagger_at_gmail.com>> wrote:
>
> Hello Experts,
>
> Could anyone explain the following command? or Point out in which
> part of the manual they are explain? .
>
> I tried to search for them on the namd website but I did not find
> anything?
> I dont understand inside the loop pmf {} and what are they are
> they 3 pmf serial.
>
> thanks
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # conformational free energies
> ### 10 ps growing time as per NAMD user guide example
> ### use pulling speed of 0.1 A/ps as per NAMD tutorial, p. 68
> freeEnergy on
> freeEnergyConfig {
> urestraint {
> dist pmf (BH, 1, N) (BH, 10, NT) kf=7.2 low=13 hi=33
> }
> pmf {
> task = grow
> time = 10 ps
> }
> pmf {
> task = up
> time = 200 ps
> print = 1 ps
> }
> pmf {
> task = stop
> time = 10 ps
> }
> pmf {
> task = down
> time = 200 ps
> print = 1 ps
> }
> }
>
>
>
> --
> Pedro
>
> Saludos
>
> Departamento de Física,
> Facultad de Ciencias,
>
> Universidad de Chile
> Las Palmeras 3425, Ñuñoa, Santiago, Chile
>
>
>
>
> --
> Pedro
>
> Saludos
>
> Departamento de Física,
> Facultad de Ciencias,
>
> Universidad de Chile
> Las Palmeras 3425, Ñuñoa, Santiago, Chile
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