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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Received on Wed Feb 10 2010 - 09:00:03 PST
