Thanks a lot for suggestion now, i am getting equilibrated cubic water box.
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> 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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>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Feb 13 2010 - 01:00:04 PST
