People usually seem to like it better if you try and then puzzle over an
error or a result, than if you ask them to just review something.
Bill
On 9/12/18 1:36 PM, Saikat Pal wrote:
>
> Sent from Yahoo Mail on Android
>
> ----- Forwarded message ----- From: "Saikat Pal" <saikatpaliitg.yahoo.com> To: "AMBER Mailing List" <amber.ambermd.org> Cc: Sent: Wed, 12 Sep 2018 at 12:39 PM Subject: Query for umbrella sampling Dear all,I want to calculate the PMF of two peptides. I want to pull two atoms along the Z axis. I want to know is my input is correct or not ?:4000 step minimization for 15 ang
> #minimisation
> &cntrl
> imin = 1,
> maxcyc=4000, ncyc = 1000,
> ntpr = 100, ntwr = 1000,
> ntf = 1, ntc = 1, cut = 10.0,
> ntb = 1, ntp = 0,
> nmropt = 1,
> &end
> &wt
> type='END',
> &end
> DISANG=disang.15
>
> #equilibration1000 ps NPT equilibration for 15 ang
> &cntrl
> imin = 0, ntx = 1, irest = 0,
> ntpr = 5000, ntwr = 50000, ntwx = 0,
> ntf = 2, ntc = 2, cut = 10.0,
> ntb = 2, nstlim = 500000, dt = 0.002,
> tempi=0.0, temp0 = 298.0, ntt = 3,
> gamma_ln = 1.0,
> ntp = 1, pres0 = 1.0, taup = 5.0,
> nmropt = 1, ioutfm=1,
> &end
> &wt
> type='END',
> &end
> DISANG=disang.15
>
> #production10 ns NPT production for 15 ang
> &cntrl
> imin = 0, ntx = 5, irest = 1,
> dielc=1.0,cut=10.0,
> ntt=1,temp0=298.0,tautp=0.1,
> ntp=1,ntb=2,ntc=2,ntf=2,
> iwrap=1,nstlim=5000000,dt=0.002,
> ntwx=1000,ntpr=500,nmropt=1,
> pres0 = 1.0,
> &end
> &wt
> type='DUMPFREQ', istep1=10,
> &end
> &wt
> type='END',
> &end
> DISANG=disang.15
> DUMPAVE=distance_15.dat
>
> #disang#Harmonic restraints for 15 ang
> &rst
> iat=-1,-1,
> iresid=1,
> r1=-99.00000, r2=15.00000, r3=15.00000, r4=99.00000,
> rk2=6.0, rk3=6.0,
> igr1=6,0,
> igr2=1,1,0,
> grnam1(1)='O14',
> grnam2(1)='N1',grnam2(2)='N3',
> /
>
>
>
>
> Thanks and Regards,
> Saikat Pal
>
>
>
>
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Received on Wed Sep 12 2018 - 14:00:03 PDT
