Hi, Lyndon LS Meng
For wall restraint you can try &pmd module, in your case you can add like
the following section
&pmd
monitor_file = 'pmd.dat'
monitor_freq = 500
anchor_position = 0.0, 25.0,100.0,110
anchor_strength = 500.0,500.0
cv_file = 'cv_pmd.dat'
&
and define your pmd CV in cv_pmd.dat
you can check manual section 25.4.4
if you are using Amber22 or newer, the efficiency if improved
On Fri, Feb 14, 2025 at 5:32 AM 孟令屾 via AMBER <amber.ambermd.org> wrote:
> Dear Amber Support Team,
>
> I am currently running Metadynamics simulations using ABMD with wall
> restraints and have encountered a significant performance issue. My setup
> is as follows:
>
> I'm using ABMD with FLOODING mode for a COM_DISTANCE collective variable:
>
> codeCopy code
>
> &abmd
> mode = 'FLOODING'
> timescale = 100.0
> monitor_file = 'abmd.dat'
> monitor_freq = 500
> cv_file = 'cv.dat'
> wt_temperature = 10000.0
> wt_umbrella_file = 'wt_umbrella.nc'
> /
>
>
> The CV is defined as:
>
> codeCopy code
>
> &colvar
> cv_type = 'COM_DISTANCE'
> cv_ni = 5590
> cv_i = …
> cv_min = 20.0
> cv_max = 110.0
> resolution = 0.10
> /
>
>
> I've implemented wall restraints using a distance restraint file
> (disang.rst):
>
> codeCopy code
>
> &rst
> iat = -1, -1,
> igr1 = ...
> igr2 = ...
> r1 = 0.0,
> r2 = 25.0,
> r3 = 100.0,
> r4 = 110.0,
> rk2 = 500.0,
> rk3 = 500.0,
> &end
>
> After implementing these wall restraints, I've observed a dramatic
> decrease in performance from 220 ns/day to 72 ns/day.
>
>
>
>
> I'm wondering if there's a more efficient way to implement these
> boundaries, perhaps similar to PLUMED's uwall and lwall settings where the
> CVs can be directly used for the restraints?
>
> Any suggestions for improving the performance while maintaining the wall
> restraints would be greatly appreciated.
>
> Thank you for your time and assistance.
>
> Best regards,
>
>
>
>
>
> Lyndon LS Meng
>
>
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>
--
Feng Pan
Senior Research Scientist
Email: fpan3.ncsu.gmail.com; fpan3.alumni.ncsu.edu
*(The email fpan3.ncsu.edu <fpan3.ncsu.edu> will be disabled soon, please
use fpan3.ncsu.gmail.com <fpan3.ncsu.gmail.com> or fpan3.alumni.ncsu.edu
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Received on Tue Feb 18 2025 - 10:30:03 PST
