Hi,
It could be you are pulling too fast with a high strength, try to reduce
the harmonic
strength of pulling and also extend your simulation time.
Best
Feng
On Thu, Aug 30, 2018 at 6:06 AM M RCC <mkr3j2c1.gmail.com> wrote:
> Dear Amber users
> I did SMD of protein ligand complex (20A from the initial position), and
> in the result file the work for pulling the ligand is keep on incresing as
> regard with the distance!,
> I am expecting plot such the force will increase while pulling the ligand
> out from the cavity then decrease after the ligand came out of the cavity.
>
> Am I doing correctly? i still need a clarification about this!
>
> I have pasted the result file and input files am using for pulling the
> ligand out from protein.
>
> """
> 8.13800 9.23098 -218.59562 0.00000
> 8.21800 8.25037 -6.47449 -0.54583
> 8.29800 8.31760 -3.92022 -0.88007
> 8.37800 8.47082 -18.56317 -1.00396
> 8.45800 8.50562 -9.52336 -1.24856
> 8.53800 8.56110 -4.61905 -1.45729
> ............
> 26.93800 26.99166 -10.73237 54.68420
> 27.01800 26.99442 4.71645 54.74462
> 27.09800 27.15913 -12.22665 54.79492
> 27.17800 27.18728 -1.85637 54.79982
> 27.25800 27.24111 3.37721 54.89353
> 27.33800 27.36441 -5.28141 54.91381
> 27.41800 27.40588 2.42494 55.05123
> 27.49800 27.46560 6.47983 55.19436
> 27.57800 27.49030 17.54008 55.16678
> 27.65800 27.68766 -5.93276 55.14094
> 27.73800 27.71692 4.21613 55.02136
> 27.81800 27.78315 6.97099 55.08781
> 27.89800 27.85140 9.32058 55.03641
> 27.97800 27.96085 3.42948 55.11920
> 28.05800 28.11506 -11.41155 55.15004
> """"""
>
> and i have used the input parameters as
>
> ############
>
> pulling
> &cntrl
> imin=0, ntx=5, irest=1,
> ntc=2, ntf=2, tol=0.0000001,
> nstlim=250000, ntt=3, gamma_ln=1.0,
> temp0=303.0,
> ntpr=1000, ntwr=500000, ntwx=1000,
> dt=0.002, ig=-1,
> ntb=2, cut=10.0, ioutfm=1, ntxo=2,
> nmropt=1, ntp=3, csurften=3, gamma_ten=0.0, ninterface=2, jar=1,
> /
> &wt type='DUMPFREQ', istep1=1000 /
> &wt type='END', /
> DISANG=COM_pull.RST
> DUMPAVE=05_Pull_dist.dat
> LISTIN=POUT
> LISTOUT=POUT
> /
> /
> &ewald
> skinnb=3.0,
> /
>
> #########
> .rst file
> &rst
> iat=4311,3473,
> r2=8.138,
> rk2=100,
> r2a=28.138,
> /
> ############
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Fri Aug 31 2018 - 15:30:02 PDT
