Hi,
Thanks alot. I did the equilibration with weak restrain (only 2) and then
did not found any bubble. Now the equilibration seems quite well.
I am doing this MD simulation for MM-PB/SA calculation so can anyone have
experience with simulation condition of production run ?
I did heating in NVT, equilibration in NPT ensamble. Will it be ok if i
switch to NVT or NVE for production run. In tutorial B1 (simulation a small
fregment of DNA) it has been described to use NVT or NVE in production run
but in advance tutorial for MM-PB/SA it has been mentioned that "The
production phase of the simulation should be run using the same conditions
as the final phase of equilibration to prevent an abrupt jump in the
potential energy due to a change in simulation conditions."
I think energy jump is the main issue behind it and if I use different
ensemble but not having any abrupt energy jump then it should be fine. I
wold like to ask ur suggestion about input parametres for production run, I
was thinking to use NVT with Berendsen temperature coupling scheme. Please
suggest as per your experiences. I will be happy if u will mark the
parametres in fallowing production.in file according to your suggestions.
######################### PRPDUCTION RUN ###############################
production run at NVT
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1000000,dt=0.001,
ntc=2,ntf=2,ioutfm=1,
cut=10.0, ntb=2, ntp=1, taup=5.0,
ntpr=1000, ntwx=1000,
ntt=1 ,
temp0=300,
/
EOF
thanking you in agvance.
..mish
On Sat, May 8, 2010 at 1:07 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it's possible that the restraint force constant is too high, or
> perhaps you have problems with the force field parameters for the
> ligand (if you have one).
> it's very hard to say from the current info. I think you need to
> carefully analyze the output file. what is the pressure? what about
> temperature? are these both the values that you requested? it seems to
> be having problems equilibrating, but the bubble is probably a symptom
> and you need to analyze the output to find the initial problem.
>
> On Sat, May 8, 2010 at 6:55 AM, mish <smncbr.gmail.com> wrote:
> > 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
> >> >> >> > _______________________________________________
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Received on Wed May 19 2010 - 07:30:03 PDT
