Your plan sounds reasonable, depending on the structures that you obtained
from the TMD. Did you look at the outputs? Do you actually achieve low rmsd
at the end? That can be challenging. NEB depends strongly on the endpoint
structures, so if you feel those are good representation then go ahead with
NEB.
On Fri, Apr 20, 2018, 5:33 AM Aravind Ravichandran <raravind.ibab.ac.in>
wrote:
> 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,Any help is appreciated and thanks in
> advance!!
>
> ---------------------------------------------------------
> Aravind R
> National Center for biological sciences
> Banglore, India
> /
> &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 - 05:00:03 PDT
