Hi,
Fixed means restrained. but used very tight restrain (restraint_wt=200.0).
I used proper ensembles mentioned in literature. But I am copying detail of
input file so that u can point out other mistakes too..
------------ -------Step 1 ---------------------------
minimization of solvent molecules
&cntrl
imin=1,maxcyc=3000,ncyc=500,
cut=10.0,ntb=1,
ntc=1,ntf=1,
ntpr=50,
ntr=1, restraintmask=':1-266',
restraint_wt=200.0,
/
------------------- step 2 --------------------------
heating system with fixed protein
&cntrl
imin=0,irest=0,ntx=1,
nstlim=300000,dt=0.001,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
tempi=10.0, temp0=300,
ntr=1, restraintmask=':1-266',
restraint_wt=200.0,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=250000,
value1=10.1, value2=300, /
&wt TYPE='END' /
------------------- step 3 --------------------------equilibrating water in
the system with fixed protein
&cntrl
imin=0,irest=1,ntx=5,
nstlim=700000,dt=0.001,
ntc=2,ntf=2,
cut=10.0, ntb=2, ntp=1, taup=5.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300,
ntr=1, restraintmask=':1-266',
restraint_wt=200.0,
/
and i can see that weired behavior after step 3, which i supposed to be
proper equilibrated octahedral box after 70 ps equilibration.
....mish
On Thu, May 6, 2010 at 2:28 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> you don't say the most important thing- did you use NVT or NPT in each
> step? and when you say "fixed", do you mean frozen or restrained?
>
> On Thu, May 6, 2010 at 8:00 AM, mish <smncbr.gmail.com> wrote:
> > Hi all :
> >
> > I am trying to do some MM-PB/SA calculation in my system. For
> equilibration
> > of the salivated system (octahedral TIP3P) i used the fallowing scheme-
> > 1- Minimization of solvent molecules with fixed protein
> > 2- Heating system with fixed protein (300 ps)
> > 3- Equilibrating water in the system with fixed protein (700 ps)
> > 4- Minimization of protein with with fixed water
> > 5- Heating system with fixed water (300ps)
> > 6- Equilibration of whole system without any restrain (10 ns)
> >
> > I found that the density in the step 6 is less than 1 for first few few
> ps
> > and then it adjust is very soon. When i look in adjustment of water
> molecule
> > after each step, I found a weird thing after step 3. I did imaging with
> > ptraj and found that few planes of octahedral water-box have small well
> > shaped arrangenemt of water. I am really surprised that why this
> happened.
> > Is it may be due to only 12A layer of water box, that PBC is showing
> effcet
> > of adgacent protein ?
> >
> > Reigards
> >
> > ..mish
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> >
>
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Received on Thu May 06 2010 - 06:00:07 PDT
