see section 20.4 of the Amber18 manual - you should be using tgtfitmask and
tgtrmsmask but I only see tgtrmsmask in your input.
I'm not sure what would happen when you also turn on positional restraints
as you have done here (using ntr=1 and restraintmask)- it might work, but
it might not depending on how that matches the other masks. I don't have
the ability to check the code right now.
what does the beginning of the output say about the targeted md part? does
it give a fitmask?
to check and see if it's working, the best way is to use cpptraj to do the
rmsd fit to the same reference structure that you gave the md code, using
the same mask as you use for tgtfitmask, and then calculate the rmsd next
using the tgtrmsmask but including the "nofit" flag. The resulting data
stream should match what you asked the md to do (though it's unlikely that
it can reach exactly 0 rmsd).
On Mon, Nov 26, 2018 at 3:22 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 - 13:00:02 PST
