From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 29 2016 - 10:20:36 CST
Or quite simply, you can do as Jérôme suggested and simply avoid using
options not recommended and disabled by default.
However, I suspect that you will end up turning on outputTotalForce anyway
(which is useful in many cases), and may be puzzled by the different
numbers coming out of NAMD 2.12b1 vs. previous versions.
"Standard" ABF still works in the new version, please go ahead and use it.
Giacomo
On Tue, Nov 29, 2016 at 11:12 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Hi,
>
> The answer is simple: you don't need any of those options. You are doing
> "standard" ABF with no complicated tricks, so all the defaults will work
> for you.
>
> Best,
> Jerome
>
> On 29 November 2016 at 16:39, Bala subramanian <bala.biophysics_at_gmail.com>
> wrote:
>
>> Friends,
>> My aim is the following, a) Study the pmf of a single potassium ion
>> through a channel, b) Study the pmf of a single potassium ion in the
>> presence of additional ion. The objective is to calculate the force (along
>> the reaction coordinate) on my testing ion in the absence and presence of
>> additional ion, and also the PMF profile.
>>
>> colvarsTrajFrequency 500
>> colvarsRestartFrequency 500
>> colvar {
>> name Translocation
>> width 0.2
>> lowerboundary -4.0
>> upperboundary -1.0
>> lowerwallconstant 20.0
>> upperwallconstant 20.0
>> distanceZ {
>> main {atomnumbers { 16625 } # My testing ion
>> ref { atomnumbers { 2025 7565 13105 }
>> }
>> axis ( 0.0, 0.0, 1.0 ) }
>> }
>>
>> colvar {
>> name Additional
>> width 0.2
>> lowerboundary -9.0
>> upperboundary -7.0
>> hardLowerBoundary yes
>> hardUpperBoundary yes
>> lowerwallconstant 20.0
>> upperwallconstant 20.0
>> distanceZ {
>> main { atomnumbers { 16624 } # additional ion from my testing ion
>> }
>> ref { atomnumbers { 16625 }
>> }
>> axis ( 0.0, 0.0, 1.0 )
>> }
>> }
>>
>> abf {
>>
>> colvars Translocatio
>>
>> fullSamples 800
>>
>> historyFreq 500
>>
>> }
>>
>> a) Which is the correct colvar option that I should choose to obtain the
>> correct force on my testing ion *OutputTotalForce* or *oneSiteTotalForce*
>>
>> b) I am using latest namd version, the manual says that there is a
>> *subtractAppliedForce* option available, but it is not recommended.
>>
>> There is also *ouputAppliedforce* option. Should i simply obtain the
>> totalfoce and subtract the appliedforce to remove any force due to bias ?
>>
>> Could you please guide which options should I use to achieve my
>> objective.
>>
>>
>> --
>> C. Balasubramanian
>>
>
>
-- Giacomo Fiorin Associate Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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