Re: Question about applying external force

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Mar 06 2017 - 15:40:38 CST

Hello Sebastian, scriptedColvarForces is not a NAMD keyword, and should not
be included in the main configuration file. It is provided by the Colvars
module instead.

On Mon, Mar 6, 2017 at 4:32 PM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:

> Thanks for your reply, Jerome! I'm getting issues with this command
> (ERROR: The following variables were set in the
> configuration file but are NOT VALID:scriptedColvarForces).
> This is what I wrote:
>
> #CONSTRAINTS#
> scriptedColvarForces on
> colvars on
> colvarsConfig separation.in
>
> #SCRIPT
> numsteps 20000
>
> proc calc_colvar_forces { ts } {
> set omega 42.
> set A 42.
> cv colvar d1 addforce [expr {$A * cos($omega * $ts)}]
> }
>
>
> and I defined d1 in separation.in:
>
> colvarsTrajFrequency 1
> colvarsRestartFrequency 1
> colvar {
> name d1
>
> distance {
> group1 {
> atomNumbersRange 1-28
> }
> group2 {
> atomNumbersRange 411-444
> }
> }
> }
>
>
> Any idea of what am I doing wrong? Also, can I do this procedure for two
> molecules simultaneously?
>
> On Mon, Mar 6, 2017 at 3:23 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
>> Hi Sebastian,
>>
>> This sounds like a job for a scripted collective variable restraint.
>> <http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-810006.10>
>>
>> Define a variable named d made of a distance component between the two
>> molecules, enable scriptedColvarForces, and then this Tcl procedure
>> should do the trick:
>>
>> proc calc_colvar_forces { ts } {
>> set omega 42.
>> set A 42.
>> cv colvar d addforce [expr {$A * cos($omega * $ts)}]
>> }
>>
>>
>> Best,
>> Jerome
>>
>>
>> On 6 March 2017 at 20:56, The Cromicus Productions <
>> thecromicusproductions_at_gmail.com> wrote:
>>
>>> Hi everyone,
>>>
>>> I would like to consider the center of mass of two molecules and apply a
>>> force F=Acos(wt) in the direction between the CMs to separate and get them
>>> back. Is this possible in NAMD? Any suggestion about how to do it?
>>> Thank you very much,
>>>
>>> Sebastian
>>>
>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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