Hi,
I tried 100ps equilibration at strong pressure coupling ( at taup = 0.1) but
still getting those patterns and density is less than 1 after the equil.
What could be other possible reason behind this patter like vacuum bubbles
?
reg
...mish
On Fri, May 7, 2010 at 12:43 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it looks to me like the pressure might not be equilibrated and the
> density is low. the patterns look like vacuum bubbles.
> try to do your water equilibration step with a strong pressure coupling
> (0.1).
>
>
>
> On Fri, May 7, 2010 at 12:59 AM, mish <smncbr.gmail.com> wrote:
> > Hello Dr Simmerling
> > There is prmtop and mrcrd of from the last snapshot from step3. u can
> have a
> > look in vmd because from a sinle pic u might not see the problem in all
> > planes. Step 3 final density is slightly less than 1.
> > scripts for ptraj i used is -
> > -----------------ptraj.in----------------
> > trajin step3.rst
> > center :1-266 mass origin
> > image center familiar com :1-266
> > trajout step6last_img.rst
> > ----------------------------------------------
> > Thanking u ..
> > ...mish
> > On Thu, May 6, 2010 at 6:31 PM, Carlos Simmerling
> > <carlos.simmerling.gmail.com> wrote:
> >>
> >> step 3 seems ok- maybe a picture would help us understand what you see.
> >> make sure the ptraj imagine is done correctly. is the step 3 final
> >> density ok? the pressure coupling is pretty weak.
> >>
> >>
> >> On Thu, May 6, 2010 at 8:56 AM, mish <smncbr.gmail.com> wrote:
> >> > 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
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 08 2010 - 04:00:03 PDT
