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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Received on Wed Oct 13 2010 - 07:30:12 PDT
