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 - 12:30:03 PST
