From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Mon Mar 06 2017 - 18:27:20 CST
Thanks! I think I got it to work
On Mon, Mar 6, 2017 at 5:23 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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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