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
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>
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Received on Wed Oct 13 2010 - 07:30:15 PDT
