Dear Amber users,
I am trying to run targeted MD to study conformational changes during the simulation between initial and final structure of a protein. As I run the simulation the structure moves from initial position to the final structure, but it doesn't 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. The input file and movies for the simulation have been attached. I aligned the target structure in the movies, so you can follow its movement.
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",
/
Dropbox links for movies:TMD1.mp4
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TMD1.mp4
Shared with Dropbox
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TMD2.mp4
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TMD2.mp4
Shared with Dropbox
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Received on Sat Nov 24 2018 - 04:00:02 PST
