Dear Amber Users/Authors,
I am intending to perform NEB simulations for finding low energy pathways
for transition between an open and close form of a protein. I have already
performed TMD simulation from open to close form.
Now, can I generate multiple snapshots along the TMD trajectory and use it
as an input for simulated annealing and NEB, after a thorough minimization
on the
structures??
Or is it better to do generate replicas by heating, as mentioned in the
manual so that the process is random and not biased??
Will results differ in both the cases??
This is how I ran my TMD simulation(10ns, with equilibration in between).
Ubi targeted MD
&cntrl
imin = 0, nstlim = 5000000, dt = 0.002,
ntx = 1, ntt = 3, gamma_ln = 1.0,
ntc = 2, ntf = 2, ntb = 2, ntp=1,
cut = 10.0, nscm = 0,
ntpr = 1000, ntwx = 1000, ntwr = 1000,
igb = 0, irest=0, nmropt=1,tempi=300.0,
itgtmd=1, tgtmdfrc=0.25,
tgtfitmask=":77-222.CA,N,C,O",
tgtrmsmask=":1-70.CA,N,C,O",
/
&wt
TYPE='TGTRMSD', istep1 =0, istep2 = 400000,
value1 = 40.957, value2 = 35.0,
/
&wt
TYPE='TGTRMSD', istep1 =400001, istep2 = 600000,
value1 = 35.0, value2 = 35.0,
/
&wt
TYPE='TGTRMSD', istep1 =600001, istep2 = 1000000,
value1 = 35.0, value2 = 30.0,
/
&wt
TYPE='TGTRMSD', istep1 =1000001, istep2 = 1200000,
value1 = 30.0, value2 = 30.0,
/
&wt
TYPE='TGTRMSD', istep1 =1200001, istep2 = 1600000,
value1 = 30.0, value2 = 25.0,
/
&wt
TYPE='TGTRMSD', istep1 =1600001, istep2 = 1800000,
value1 = 25.0, value2 = 25.0,
/
&wt
TYPE='TGTRMSD', istep1 =1800001, istep2 = 2200000,
value1 = 25.0, value2 = 20.0,
/
&wt
TYPE='TGTRMSD', istep1 =2200001, istep2 = 2400000,
value1 = 20.0, value2 = 20.0,
/
&wt
TYPE='TGTRMSD', istep1 =2400001, istep2 = 2800000,
value1 = 20.0, value2 = 15.0,
/
&wt
TYPE='TGTRMSD', istep1 =2800001, istep2 = 3000000,
value1 = 15.0, value2 = 15.0,
/
&wt
TYPE='TGTRMSD', istep1 =3000001, istep2 = 3400000,
value1 = 15.0, value2 = 10.0,
/
&wt
TYPE='TGTRMSD', istep1 =3400001, istep
Any help is appreciated and thanks in advance!!
---------------------------------------------------------
Aravind R
National Center for biological sciences
Bangalore, India
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Received on Fri Apr 20 2018 - 03:00:04 PDT
