Hi Thomas,
The lattice vectors you provide are for an orthorhombic box, not a
truncated octahedron. Was your prmtop generated by leap using solvateOct?
What is the value of IFBOX in the prmtop (it should be 2 or 3)? This is in
the POINTERS section, the 3rd last value on line 3 I believe.
Regards,
Brian
On Thu, Jan 31, 2013 at 3:21 PM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> I guess this is what you mean:
>
> trajin cMDrun1.prod_TIP4PEw.nc
> center :1-162 mass origin
> image origin center familiar
> trajout cMDrun1.prod_TIP4PEw.wrapped.nc netcdf
> go
>
> The protein residues are numbered 1-162. The trajectory doesn't change, it
> seems that the barostast applies pressure over the 6 planes of a cube(?)
> instead on the 12 planes of a truncated octahedron (?). There must be
> something wrong with the parameters I am using because the .prmtop and .rst
> files look normal to me. Below is the last line of my restart (.rst) file
> from which I resumed the simulation. It was an NVT equilibration without
> restraints.
>
> 115.6172820 135.3319607 138.3907610 90.0000000 90.0000000 90.0000000
>
> I am also quoting again the relevant configuration parameters:
>
>
> ntxo=2, ! write binary NetCDF restart files
> ioutfm=1, ! use binary NetCDF format for the coordinate and velocity
> trajectory files (mdcrd, mdvel and inptraj).
> iwrap=1, ! wrap coordinates into primary box
>
> ! TEMPERATURE CONTROL
> tempi =100.0, ! initial temperature
> temp0=300.0, ! reference temperature at which the system is to be
> kept, if ntt > 0
> ntt=3, ! Use Langevin thermostat.
> gamma_ln=5, ! Damping coefficient for Langevin dynamics in ps - 1.
> tautp=2.0, ! Time constant, in ps, for heat bath coupling for the
> system, if ntt = 1
> ig=209858, ! The seed for the pseudo-random number generator
>
> ! PRESSURE CONTROL
> ntb=2, ! use constant pressure
> ntp=1, ! use pressure coupling
>
>
> Any idea what's wrong?
>
>
> Thomas
>
>
>
> On 31 January 2013 14:54, David A Case <case.biomaps.rutgers.edu> wrote:
>
> > On Thu, Jan 31, 2013, Thomas Evangelidis wrote:
> > >
> > > I ran a short simulation with pmemd.cuda using the following parameters
> > but
> > > the truncated octahedron was gradually reshaped to a parallelepiped
> box.
> > Am
> > > I doing something wrong?
> >
> > Doens't sound like it. There are various ways to represent a truncated
> > octahedron. If you want to view the results as an ocatahedron, use the
> > "familiar" keyword in the image command in ptraj or cpptraj.
> >
> > ...dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Thu Jan 31 2013 - 13:30:03 PST
