Hi, Yao
If you want to restrain your torsion between -0.4 to 2,1, you should add
the &pmd module
to restrain it, also I think that is the reason why the FE is not updating,
Best
Feng
On Thu, Mar 21, 2019 at 11:50 AM 李耀 <liyao17.mails.tsinghua.edu.cn> wrote:
> Hello Amber users,
>
>
> I'm running ABMD with NFE toolkit in pmemd. Here are one of the mdin files
> and the cv file:
>
>
> Input file for abmd
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> ntxo=1,
> ntc=2,
> ntf=2,
> nstlim=19090000,
> ntt=3,
> gamma_ln=2.0,
> tempi=300.0,
> temp0=300.0,
> ntpr=5000,
> ntwr=5000,
> ntwx=5000,
> dt=0.002,
> ig=-1,
> ntb=1,
> ntr=0,
> cut=10.0,
> ioutfm=1,
> iwrap=1,
> infe=1,
> &end
> &abmd
> mode='FLOODING'
> monitor_file='abmd_1.dat'
> monitor_freq=1000
> cv_file='cv.in'
> timescale=10.0
> umbrella_file = 'umbrella_1.nc'
> wt_temperature = 10000.0
> wt_umbrella_file = 'wt_umbrella_1.nc'
> /
>
>
> cv file:
> &colvar
> cv_type = 'TORSION'
> cv_ni = 4
> cv_i = 5653, 5639, 5620, 5551
> cv_min = -3.141593
> cv_max = 3.141593
> resolution = 0.1
> /
> &colvar
> cv_type = 'TORSION'
> cv_ni = 4
> cv_i = 5641, 5649, 5653, 3386
> cv_min = -0.4
> cv_max = 2.1
> resolution = 0.05
> /
>
>
> After processing the wt_umbrella_1.nc file with nfe-umbrella-slice, the
> cv values and free energy are dumped to FE.dat. I found that the free
> energy values in FE.dat didn't change with time. Is this reasonable? Or is
> there something wrong with my input files and structures?
>
>
> By the way, the cv_min and cv_max in the cv.in file don't seem to work,
> because the both the CVs change from -3.141593 to 3.141593. Could you
> please have a look? Thank you.
>
>
> Best,
> Yao Li
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>
--
Feng Pan
PostDoc
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Sun Mar 24 2019 - 21:00:01 PDT
