Dear Amber Users,
Please, kindly help/guide me.
Question in Brief
==============
Is there any way I can (further) strictly enforce the range of the
collectively (CV) in Adaptively Biased MD simulation? If it were to be
Steered Molecular Dynamics Simulations, I would be able to increase the
force/spring constant and drive/steer the system as I desire. Is there a
way to achieve a similar thing in ABMD? In other words, is there any
variable in ABMD that is analogous to the Force/Spring Constant in SMD and
is tunable (so that I can adjust it to more strictly enforce the range I
specified in the CV)?
I am very sorry that my question is rather too naive (maybe even stupid).
Please, also look at the additional details I provide below. Thank you very
much.
More Details
==========
I am trying to do Adaptively Biased MD Simulations (of type "COM_ANGLE"
using "FLOODING") and it appears that the range I specified for the collective
variable (CV) not "strictly" enforced. For example, I want to adaptively
force my system between cv_min = 0.3 and cv_max = 0.7 at resolution = 0.05.
(All in radians). However, when I check the monitor file, "monitor.txt", I
do NOT see my system to maintained within (or at least approximately
within) my desired range for the CV. For example, the CV dumped in the
monitor file has some values as high as 0.82 (which above 0.7 I specified)
and there is no value of the dumped CV near 0.3 that I specified (the least
value of the dumped CV I have seen so far is approximately 0.607). In other
words, I want the system to sample between 0.3 and 0.7 radians, but the
ABMD appears to be sampling between 0.6 and 0.9 radians.
Please, kindly guide me. The content of my input file "cv.in" is shown
below. I also include a section of my output/monitor file that contains
some value of the sampled CV.
++++++++++++++++++++++
#cv.in FILE#
&colvar
cv_type = 'COM_ANGLE'
cv_min = 0.3, cv_max = 0.7, resolution = 0.05
cv_ni=6
cv_i = 784, 0, 780, 813, 0, 818
/
++++++++++++++++++++++
#
# MD time (ps), CV #1, E_{bias} (kcal/mol)
#
0.9990 0.8214852146 0.0000000000
1.9990 0.8203868858 0.0000000000
2.9990 0.7514800469 0.0000000000
3.9990 0.7794953384 0.0000000000
...
242.9990 0.7524856810 0.0000000000
243.9990 0.7634033212 0.0000000000
244.9990 0.6801598169 0.0257862627
245.9990 0.8028405691 0.0000000000
246.9990 0.6577946805 0.0127113489
247.9990 0.7853694051 0.0000000000
...
1328.9990 0.8280800141 0.0000000000
1329.9990 0.7782295206 0.0000000000
1330.9990 0.6904481393 0.5377608131
1331.9990 0.7436914461 0.0000000000
1332.9990 0.8638745221 0.0000000000
1333.9990 0.7542451081 0.0000000000
1334.9990 0.6696472834 0.4234273988
++++++++++++++++++++++
With regards
Emmanuel Salawu
emmanuel.salawu.gmail.com
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Received on Wed Nov 30 2016 - 22:30:03 PST
