Re: Question about applying external force

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Mar 06 2017 - 16:23:57 CST

http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-530005.5http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-530005.5

On Mon, Mar 6, 2017 at 4:59 PM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:

> Thanks Giacomo, excuse my ignorance, I'm currently getting " FATAL ERROR:
> Setting parameter calc_calc_colvar_forces from script failed!". These are
> my files:
>
> .conf:
> ....
> #CONSTRAINTS#
>
> # ABF SECTION
>
> 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 * $ts)}]
> }
>
> separation.in:
>
> colvarsTrajFrequency 1
> colvarsRestartFrequency 1
> scriptedColvarForces on
>
> colvar {
> name d1
>
> scriptedFunction calc_colvar_forces
>
> distance {
> group1 {
> atomNumbersRange 1-28
> }
> group2 {
> atomNumbersRange 411-444
> }
> }
>
> }
>
>
>
>
> On Mon, Mar 6, 2017 at 4:40 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hello Sebastian, scriptedColvarForces is not a NAMD keyword, and should
>> not be included in the main configuration file. It is provided by the
>> Colvars module instead.
>>
>> On Mon, Mar 6, 2017 at 4:32 PM, The Cromicus Productions <
>> thecromicusproductions_at_gmail.com> wrote:
>>
>>> Thanks for your reply, Jerome! I'm getting issues with this command
>>> (ERROR: The following variables were set in the
>>> configuration file but are NOT VALID:scriptedColvarForces).
>>> This is what I wrote:
>>>
>>> #CONSTRAINTS#
>>> scriptedColvarForces on
>>> colvars on
>>> colvarsConfig separation.in
>>>
>>> #SCRIPT
>>> numsteps 20000
>>>
>>> proc calc_colvar_forces { ts } {
>>> set omega 42.
>>> set A 42.
>>> cv colvar d1 addforce [expr {$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
>>
>
>

-- 
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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