Hi George,
Are you aware that the index numbering is different in VMD compared to AMBER?
VMD index numbering starts at 0, whereas AMBER starts at 1 (same as in a pdb file). So for example atoms 2,4,6 in VMD would correspond to 3,5,7 in AMBER and so on.
Hope that is useful,
Callum
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of "Γιώργος Λαμπρινίδης" [lamprinidis.pharm.uoa.gr]
Sent: 18 September 2012 12:40
To: amber.ambermd.org
Subject: [AMBER] Monitoring Torsion Angles during MD Simulations
Dear all,
I am trying to make a long MD simulation where i need to monitor a
specific torsion angle during Simulation in order to stop it when i go
from one conformer to another one.
I got index numbers of the 4 atoms forming the torsion from vmd and i
created the following MDIN file
prod long_MD
&cntrl
imin=0,irest=1,ntx=5,
nstlim=100000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
ncsu_abmd
mode = ANALYSIS
monitor_file = 'monitor.txt'
monitor_freq = 10
variable
type = TORSION
i = (58, 50, 51, 59)
end variable
end ncsu_abmd
in the monitor.txt file i get the following:
#
# MD time (ps), CV #1
#
35446.0020 -2.4558729847
35446.0220 -2.5005559652
35446.0420 -2.5446712580
35446.0620 -2.4994620133
35446.0820 -2.6327353459
35446.1020 -2.5198900118
However i know that the starting torsion angle is -55 while on the monitor
file i get values like ~-2.5 as you can see.
The 'CV #1' values are not the torsion angle?
Or, the index numbers i got from VMD are not the correct one to use for
monitoring?
Any help would be very helpful
George
--
Dr Giorgos Lamprinidis
Researcher & Laboratory Assistant Staff
Faculty of Pharmacy
University of Athens - Greece
tel: +30 2107274304
+30 2107274824
fax: +30 2107274747
e-mail: lamprinidis.pharm.uoa.gr
geolampr.gmail.com
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Received on Tue Sep 18 2012 - 06:00:03 PDT
