Hi
I honestly do not know what the negative value will do, but in
principle, jar will compute work as the difference between two
distances, which means they both must be positive.
Perhaps take a look at
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial
in particular "*Note on windows with negative z-value"*
*
*
*Adrian*
*
*
On 4/13/26 1:46 PM, Baker, Joseph via AMBER wrote:
> [External Email]
>
> Following up on this to see if any steered MD folks have some comments.
> Thanks again!
>
> Joe
>
> ------
> Joseph Baker, PhD
> Barbara Meyers Pelson Chair in Faculty-Student Engagement (AY 2024-2027)
> Professor, Department of Chemistry
>
> On Mon, Apr 6, 2026 at 12:13 AM Baker, Joseph<bakerj.tcnj.edu> wrote:
>
>> Hello,
>>
>> We're working on a simulation where we are using the jar=1 setting to use
>> steered MD to pull a molecule through a protein channel.
>>
>> This is our RST file, and we are using the z-axis projection fxyz option.
>> The initial calculation using the cpptraj vector command for the z
>> component of the com vector between the two groups we are pulling is
>> -8.5422 angstroms (the molecule is a little below the entry to the protein
>> channel, r2 value) and then we pull it by 190 angstroms along positive z
>> (which is how we get the r2a value).
>>
>> &rst
>> iat=-1,-1,
>> r2=-8.5422 ,
>> rk2=5,
>> r2a=181.4578,
>>
>> igr2=9246,9265,9279,9286,9304,9310,9317,9339,9358,9377,9387,9398,9405,9422,9441,9461,9472,9488,9498,9519,9539,9546,9562,9578,9608,9614,9628,9647,9654,9673,9683,9702,9718,9729,9739,9758,9775,9792,9811,9827,9844,9854,19266,19285,19299,19306,19324,19330,19337,19359,19378,19397,19407,19418,19425,19442,19461,19481,19492,19508,19518,19539,19559,19566,19582,19598,19628,19634,19648,19667,19674,19693,19703,19722,19738,19749,19759,19778,19795,19812,19831,19847,19864,19874,29286,29305,29319,29326,29344,29350,29357,29379,29398,29417,29427,29438,29445,29462,29481,29501,29512,29528,29538,29559,29579,29586,29602,29618,29648,29654,29668,29687,29694,29713,29723,29742,29758,29769,29779,29798,29815,29832,29851,29867,29884,29894,39306,39325,39339,39346,39364,39370,39377,39399,39418,39437,39447,39458,39465,39482,39501,39521,39532,39548,39558,39579,39599,39606,39622,39638,39668,39674,39688,39707,39714,39733,39743,39762,39778,39789,39799,39818,39835,39852,39871,39887,39904,39914,49326,49345,49359,49366,49384,49390,49397,49419,49438,49457,49467,49478,49485,49502,49521,49541,49552,49568,49578,49599,49619,49626,49642,49658,49688,49694,49708,49727,49734,49753,49763,49782,49798,49809,49819,49838,49855,49872,49891,49907,49924,49934,
>>
>> igr1=56452,56453,56456,56458,56459,56461,56462,56464,56465,56466,56467,56470,56471,56473,56474,56475,56477,56480,
>> fxyz=0,0,1
>>
>> In the amber output file, at the beginning of the simulation it gives
>> these as the various SMD parameters
>>
>> R1 =-108.425 R2 = -8.425 R3 = -8.425 R4 = 91.575 RK2 = 5.000 RK3 =
>> 5.000
>> R1A= 81.575 R2A= 181.575 R3A= 181.575 R4A= 281.575 RK2A= 5.000 RK3A=
>> 5.000
>> Rcurr: -8.425 Rcurr-(R2+R3)/2: 0.000 MIN(Rcurr-R2,Rcurr-R3):
>> 0.000
>>
>> Those all seem to check out okay as far as I can tell, and it seems to us
>> that the molecule moves along the path we expect upon visualization with
>> VMD.
>>
>> I am just posting to see if there is anything inherently wrong with the r2
>> value being a negative number that is going to cause any subtle trouble I
>> am not considering.
>>
>> Thanks,
>> Joe
>>
>> ------
>> Joseph Baker, PhD
>> Barbara Meyers Pelson Chair in Faculty-Student Engagement (AY 2024-2027)
>> Professor, Department of Chemistry
>>
>>
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--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Apr 13 2026 - 11:30:02 PDT
