From: Pedro Swagger (pedrito.swagger_at_gmail.com)
Date: Thu Jul 25 2013 - 12:35:00 CDT
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>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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