> 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."
You could try NVT and see if energy jumps.
Bill
> 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 - 10:30:05 PDT
