no. the trajectory is fine, it's only your view of it that you might want to
change. with periodic systems it doesn't matter which unit cell the molcule
is in, but so,etimes for viewing you want them all in the main box. do that
with ptraj image command.
On Wed, Oct 13, 2010 at 11:50 AM, xue wang <xue.qfs.gmail.com> wrote:
> Thanks for your answer. So should I fix the trajectory file using ptraj
> before going to next step of simulations?
>
> Xue
>
> On Wed, Oct 13, 2010 at 10:18 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > make sure to re-image your trajectory using ptraj. search the archives
> for
> > details, this has come up many times.
> >
> >
> > On Wed, Oct 13, 2010 at 10:09 AM, xue wang <xue.qfs.gmail.com> wrote:
> >
> > > Dear Amber Users,
> > >
> > > I am having a question on the shape of water box with protein solvated
> > in.
> > > I
> > > noticed that after minimization step and before running MD the water
> box
> > is
> > > strictly cubic, but after MD runs, water box deformed to be a kind of
> > round
> > > with some water molecules far way from the majority. I checked .rst
> file
> > > after heating step and found some water molecules jumped out of the
> cubic
> > > box. Is that normal? Why would that happen? The simulation is under
> > > constant
> > > volume and periodic boundary condition. I also attached script below:
> > >
> > > Thanks for your help!
> > >
> > >
> > > *heat.in*
> > >
> > > * *
> > >
> > > 1. heat pla2-ca
> > >
> > > 2. &cntrl
> > >
> > > 3. imin=0,irest=0,ntx=1,
> > >
> > > 4. nstlim=25000,dt=0.002,
> > >
> > > 5. ntc=2,ntf=2,
> > >
> > > 6. cut=8.0, ntb=1,
> > >
> > > 7. ntpr=50, ntwx=500,
> > >
> > > 8. ntt=3, gamma_ln=2.0,
> > >
> > > 9. tempi=0.0, temp0=300.0,
> > >
> > > 10. ntr=1, restraintmask=':1-124',
> > >
> > > 11. restraint_wt=2.0,
> > >
> > > 12. nmropt=1
> > >
> > > 13. /
> > >
> > > 14. &wt TYPE='TEMP0', istep1=0, istep2=25000,
> > >
> > > 15. value1=0.1, value2=300.0,/
> > >
> > > 16. &wt TYPE='END' /
> > >
> > > * *
> > >
> > > * *
> > >
> > > *
> > > Heat_run
> > > *
> > >
> > >
> >
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> > >
> > > /common/ompi11/bin/mpiexec -machinefile $TMPDIR/machines -np $NSLOTS \
> > >
> > > $AMBERHOME/exe/sander.MPI -O -i heat.in\
> > >
> > > -p ${pdb}_solvated.top \
> > >
> > > -c min1.rst \
> > >
> > > -o heat.out \
> > >
> > > -r heat.rst \
> > >
> > > -x heat.mdcrd \
> > >
> > > -ref min1.rst \
> > >
> > > -inf Status.info \
> > >
> > > < /dev/null
> > >
> > >
> >
> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> > >
> > >
> > >
> > >
> > > Xue
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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>
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Received on Wed Oct 13 2010 - 10:00:04 PDT
