From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jul 25 2013 - 13:00:50 CDT
Pedro, you are using an input file that is three NAMD versions too old: the
"freeEnergy" command has been obsoleted since NAMD 2.7.
http://www.ks.uiuc.edu/Research/namd/2.7/ug/node47.html
If you obtained the input from a colleague, please notify him/her.
Giacomo
On Thu, Jul 25, 2013 at 1:35 PM, Pedro Swagger <pedrito.swagger_at_gmail.com>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>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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