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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Received on Mon Apr 13 2026 - 11:00:03 PDT
