On Thu, Mar 14, 2019 at 2:23 PM Ghoreishi, Delaram <delaram.phys.ufl.edu>
wrote:
> Hi Ashutosh.
>
> It is hard to tell what is going wrong without having more information
> regarding your system. Other experienced people might be able to chime in
> but here are a few thoughts:
> Did you perform simulated annealing before cooling down the system? If
> yes, did you see a smooth transition from replica 1 to replica 36?
Yes I did simulated annealing and the transition was smooth.
If yes, you probably do not even need to cool down all the way to zero, by
> equilibrating at 300 you can get a good idea about the conformational
> change you want to observe.
>
I would probably equilibrate at 300K for more time. Although when I used
108 beads instead of 36 beads transition seem to more smooth.
> Regarding your input file: since you are using shake it implies that
> hydrogen bond lengths are not important in the transition, so you can
> exclude those atoms from tgtfitmask and tgtrmsmask and save some time. In
> general, including all the atoms from residue 1 to 6227 may be overkill.
>
> Thanks for your suggestion I will modify my input file accordingly.
>
Thanks again for all the suggestion.
Ashutosh
> Best,
> Delaram
>
>
>
> ________________________________________
> From: Ashutosh Shandilya <scfbioiitd.gmail.com>
> Sent: Thursday, March 14, 2019 12:04 PM
> To: AMBER Mailing List
> Subject: [AMBER] PNEB simulation transition
>
> I ran PNEB simulation with 36 beads till heating the structure transitions
> were smooth but while cooling for the first 12 beads (frames) there is no
> change in structures(almost zero rmsd change) and from frame 13 to 36 it
> seems fine. Could anyone suggest what could be the problem.
>
> This is my input file for cooling
> --------------------------------------------------
> UDG NEB M
> &cntrl
> imin = 0, irest = 1, ntx = 5, nscm = 0,
> nstlim = 1000000, dt = 0.001, ntc = 2, ntf = 2, ig = -1,
> ntt = 3, gamma_ln = 1000.0, tempi = 300.0, temp0 = 0.0,
> ntb = 1, iwrap=1, cut = 10.0,
> tgtfitmask = ":1-6227",
> tgtrmsmask = ":1-6227",
> ineb = 1, skmin = 20, skmax = 20,
> ntpr = 5000, ntwx = 5000, ntwr = 5000,
> /
> &wt type='TEMP0', istep1=0, istep2=250000,
> value1=300.0, value2=100.0
> /
> &wt type='TEMP0', istep1=250001, istep2=500000,
> value1=100.0, value2=100.0
> /
> &wt type='TEMP0', istep1=500001, istep2=1000000,
> value1=100.0, value2=0.0
> /
> &wt type='TEMP0', istep1=1000001, istep2=2000000,
> value1=0.0, value2=0.0
> /
> &wt type='END'
> /
> Attached is the rmsd file for cooling transition.
>
> Many thanks,
> Ashutosh
> ~
>
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Received on Thu Mar 14 2019 - 12:30:02 PDT
