In addition to Callum's response regarding indices, there's probably a unit
issue here between degrees and radians.
-Dan
On Tue, Sep 18, 2012 at 9:48 PM, Dickson, Callum <
callum.dickson09.imperial.ac.uk> wrote:
> 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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>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
sindhikara.gmail.com <http://www.dansindhikara.com>
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Received on Tue Sep 18 2012 - 06:00:04 PDT
