Dear all,
Hi, I used Amber 16 (Sander.MPI) to run steered MD based on the RMSD
value of a group, but came across some wired result. In my work, I used
the RMSD of a three-atom group in the trajectory to specified reference
positions as reaction coordinate (RC). My system follows a spherical
shape and I used ibelly option to freeze those atoms far away from 15
Angstrom from the active site (the three atom group belongs to active
site).
The initial structure has the three-atom group of RMSD >1 angstrom, but
during the SMD simulation, the output CV is quite small (~0.03). I
checked the trajectory, the position of the three-atom group is >1
Angstrom away from the reference position. This makes me hardly
understand how the "MULTI_RMSD" works in amber, or I made some mistake
in the input.
In the mail archive, I found a topic related to my question:
http://archive.ambermd.org/201803/0162.html. Since there is no further
update on that topic, it is not easy for me to spot what is going on.
Any advice and help is greatly appreciated.
Parameter file:
A NVT simulation for common production-level simulations
&cntrl
imin=0, irest=0, ntx=1,
ntt=1, tautp=0.2, tempi=0.0, temp0=300.0,
ntb=0, cut=10.0,
nstlim=50000, ! 50K steps, 100 ps total
dt=0.002, ntc=2, ntf=2,
ntpr=1000, ntwx=10000, ntwr=10000, ntxo=2,
ioutfm=1, !
watnam='WAT', owtnm='O',
ibelly=1, bellymask=':140.2235<:15.0',
infe=1
/
&smd
output_file='output.00'
output_freq=50
cv_file='cv.in'
/
The cv.in has the following content:
cv_file
&colvar
cv_type = 'MULTI_RMSD'
cv_ni = 4, cv_nr = 9,
cv_i = 7418,7419,7420,0
cv_r =-0.961, 6.247, 1.144,
-0.714, 6.189, 2.400,
-0.171, 5.716, 0.297
! cv_min=0,cv_max=5
npath=2,path =1.0, 0.0
nharm=1,harm=100.0
/
------------------------------------------------------------
BTW, the coordinate of atom 7418, 7419, 7420 in the input is :
ATOM 7418 CD GLU 471 0.717 6.595 1.996 1.00
0.00 C
ATOM 7419 OE1 GLU 471 1.248 7.407 2.830 1.00
0.00 O
ATOM 7420 OE2 GLU 471 0.160 5.570 2.423 1.00
0.00 O
The output.00 has follows:
#
# MD time (ps), CV, handle_position, spring_constant, work
#
0.0000 0.02268009 1.00000000 100.00000000 0.00000000
0.1000 0.04893004 0.99999700 100.00000000 -0.00028010
0.2000 0.07148906 0.99998802 100.00000000 -0.00113452
(CV is quite small)
Thanks
xiaoyong
KU Leuven
Belgium
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Received on Thu May 28 2020 - 09:00:03 PDT
