Re: [AMBER] Monitoring Torsion Angles during MD Simulations

From: Giorgos Lamprinidis <lamprinidis.pharm.uoa.gr>
Date: Tue, 18 Sep 2012 16:05:57 +0300

Many Thanks, Dan and Callum,

You were write both, I missed the radian part.... I changed the numbering
and now everything is fine! CHEERS!!!!!

George


-----Original Message-----
From: Dickson, Callum [mailto:callum.dickson09.imperial.ac.uk]
Sent: Tuesday, September 18, 2012 3:48 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Monitoring Torsion Angles during MD Simulations

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 - 06:30:05 PDT
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