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
> >
> _______________________________________________
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>
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Received on Wed Oct 13 2010 - 09:00:04 PDT
