links to the movies:
https://www.dropbox.com/s/weezo4c1hmoc68j/TMD1.mp4?dl=0
https://www.dropbox.com/s/htjdlyuohlglxt5/TMD2.mp4?dl=0
On Mon, Nov 26, 2018 at 11:51 PM M. Reza Ganjalikhany <
ganjalikhany.gmail.com> wrote:
> Dear Amber users,
>
> I am trying to run targeted MD to study a large conformational change
> during the simulation between two states of a protein. As I check the
> movies from the trajectories, I see that the structure moves from initial
> to the final structure, but it does not stop at the final point and it
> continues to move further beyond the final position. Also, the moving part
> of the structure hits other parts of the protein and I realize that this
> movement will not show the low energy path between the initial and final
> conformations.
> I have changed the parameters but I couldn't solve the problem. Since I
> performed short simulations to see the results quickly, I am not sure
> whether I have to set large number for *nstlim *or reduce the *tgtfrc ? *Is
> there any other parameter which is neglected or should be defined in the
> input file? The input file has been attached. I wanted to send the movies
> but it is not possible due to the limitation is the email size.
>
> I appreciate you valuable comment to tackle this problem.
>
> Regards,
>
> Input parameters for targeted MD:
> TMD icl2
> &cntrl
> imin = 0, ntx = 1, nstlim = 12000, irest=0, dt = 0.002, ntc = 2, ntf =
> 2, tol = 0.000001, tempi = 100.0, temp0 = 300.0, cut = 10.0,
> ntpr = 10, ntwx = 10, ntwr = 100, ntb = 0, ntt = 1, tautp = 0.5, ntp =
> 0, igb = 1, nscm = 0, nmropt = 1, ntr = 1, restraint_wt=0.02,
> itgtmd = 1, tgtrmsd = 39.553, tgtmdfrc = 0.005, restraintmask=
> ":1-114,131-166,188-204,229-249,448-577.CA"
> tgtrmsmask= ":115-130,167-187,205-228,250-447,578-775.CA",
> /
> &wt
> TYPE='TGTRMSD', istep1=1, istep2=8000,
> value1 = 0.0500, value2 = 0.0,
> /
> &wt
> TYPE='TGTRMSD', istep1=8000, istep2=12000,
> value1 = 0.0, value2 = 0.0,
> /
> &wt
> type="END",
>
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Received on Mon Nov 26 2018 - 12:30:04 PST
