Hello,
For periodic boundary conditions (ntb=1 or ntb=2), you need to use the
variable "iwrap=1" to keep all particles in the same periodic box.
The box is not really changing shape/size (it may change size slightly
for constant pressure simulations, but not considerably if
equilibration/setup was done carefully). The problem is that without
iwrap=1, the waters are diffusing out of the initial box and not being
re-imaged back on the other side. There are plenty of discussions on
the mailing list about this variable.
Good luck!
Jason
On Wed, Feb 10, 2010 at 11:48 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
> Hello
>
> I am new user for Amber, simulating cubic water box.
>
> solvateBox wat TIP3PBOX {12 12 12}
> Solute vdw bounding box: 3.726 3.695 3.537
> Total bounding box for atom centers: 27.726 27.695 27.537
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 30.975 30.860 30.276 angstroms.
> Volume: 28940.244 A^3
> Total mass 11025.792 amu, Density 0.633 g/cc
> Added 611 residues
>
> First I minimize the water box and here is input:
>
> initial minmization prior MD
> &cntrl
> imin=1,
> maxcyc=5000,ncyc=2000,
> ntb=1,cut=8
> /
>
> Then i did gradual heating form 0-300K using NVT ensemble,here is the input:
>
> MD
> &cntrl
>
> imin=0,nstlim=300000,dt=.001,ntpr=200,ntwx=200,
> ntx=1,ntt=3,gamma_ln=1,cut=8,ntb=1,tempi=0,nmropt=1
> &end
> &wt
> type='TEMP0', istep1=0, istep2=20000, value1=0, value2=20,
> &end
> &wt
> type='TEMP0', istep1=20001, istep2=40000, value1=20, value2=40,
> &end
> &wt
> type='TEMP0', istep1=40001, istep2=60000, value1=40, value2=60,
> &end
> &wt
> type='TEMP0', istep1=60001, istep2=80000, value1=60, value2=80,
> &end
> &wt
> type='TEMP0', istep1=80001, istep2=100000, value1=80, value2=100,
> &end
> &wt
> type='TEMP0', istep1=100001, istep2=120000, value1=100, value2=120,
> &end
> &wt
> type='TEMP0', istep1=120001, istep2=140000, value1=120, value2=140,
> &end
> &wt
> type='TEMP0', istep1=140001, istep2=160001, value1=140, value2=160,
> &end
> &wt
> type='TEMP0', istep1=160001, istep2=180001, value1=160, value2=180,
> &end
> &wt
> type='TEMP0', istep1=180001, istep2=200000, value1=180, value2=200,
> &end
> &wt
> type='TEMP0', istep1=200001, istep2=220001, value1=200, value2=220,
> &end
> &wt
> type='TEMP0', istep1=220001, istep2=240000, value1=220, value2=240,
> &end
> &wt
> type='TEMP0', istep1=240001, istep2=260001, value1=240, value2=260,
> &end
> &wt
> type='TEMP0', istep1=260001, istep2=280000, value1=260, value2=280,
> &end
> &wt
> type='TEMP0', istep1=280001, istep2=300000, value1=280, value2=300,
> &end
> &wt
> type='END'
>
> Next I did equilibration using NVT ensemble and here is input:
>
> MD
> &cntrl
> imin=0,
> irest=1,ntx=7,
> ntwx=200,ntpr=200,
> ntb=1,cut=8,
> nstlim=100000,dt=.001,
> ntt=3,gamma_ln=1
> temp0=300.0,tempi=300.0
>
>
> Then i did second,third & fourth equilibration using NPT ensemble and here are
> input:
>
> MD
> &cntrl
> imin=0,
> irest=1,ntx=7,
> ntwx=200,ntpr=200,
> ntb=2,cut=8,
> nstlim=500000,dt=.001,
> ntt=3,gamma_ln=1
> temp0=300.0,tempi=300.0,
> ntp=1,pres0=1.0,taup=2.0
>
>
> MD
> &cntrl
> imin=0,
> irest=1,ntx=7,
> ntwx=200,ntpr=200,
> ntb=2,cut=8,
> nstlim=100000,dt=.001,
> ntt=3,gamma_ln=1
> temp0=300.0,tempi=300.0,
> ntp=1,pres0=1.0,taup=2.0
>
>
> MD
> &cntrl
> imin=0,
> irest=1,ntx=7,
> ntwx=200,ntpr=200,
> ntb=2,cut=8,
> nstlim=300000,dt=.001,
> ntt=3,gamma_ln=1
> temp0=300.0,tempi=300.0,
> ntp=1,pres0=1.0,taup=2.0
>
>
> Now when i am visualizing the water box after heating and equilibration shape of
> box is changing.
> Water molecules subtracted during heating at 0-300K so shape of box is changing,
> after equilibration for 500ps water molecules dispersed and slightly regain the
> cubic shape but when again equilibrate for 100ps & 300ps become spherical.
> Since shape of water box is changing during equilibration i am not getting the
> equilibrated cubic water box.
>
> So anybody suggest how to get equilibrated water box.
>
> With due regards
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Feb 10 2010 - 09:00:04 PST
