Hello,
How do you know this is the wrong behavior? Again, have you visualized your
system to see what's happening? Are all other parameters besides the
constant pH parameters the same between both simulations? Have you applied
all of the bug fixes? This was particularly a problem before bug fixes for
constant pH were submitted.
Hope this helps,
Jason
On Wed, Jul 28, 2010 at 3:06 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> By mistake i did constant protonation without restraint
> but now i have used same restraint on both constant protonatioon and
> constant pH.
>
> Minimization = 10.0, heating = 2.0, and in equilibration = 0
> Still i am getting high RMSD in 2.5ns run.
>
> maximum rmsd in constant protonation = 18
> maximum rmsd in constant pH = 7
>
> Here i am using hydrogen add crystal structure as reference and it is for
> CA,N,C,O.
> Here are input file what i have used
>
> Minimization
>
> minimization of entire system
> &cntrl
> imin=1,igb=2,
> maxcyc=3000, ncyc=1000,
> cut=30,ntb=0,ntr=1,
> restraintmask='.CA,N,O,C',restraint_wt=10.0
> /
>
>
>
> Heating
>
> MD 300ps
> &cntrl
> imin=0,
> irest=0,ntx=1,ntb=0,cut=30,
> ntpr=500,ntwx=500,ntwr=500,
> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> nstlim=150000,dt=.002,ntr=1,
> ntt=1,tempi=0,temp0=300,nmropt=1,
> scee=1.2,saltcon=0.1,tol=0.000001,
> icnstph=1,solvph=4,ntcnstph=5,
> restraintmask='.CA,N,C,O',restraint_wt=2.0
> &end
> &wt
> type='TEMP0', istep1=0, istep2=10000, value1=0, value2=20,
> &end
> &wt
> type='T..........
>
> Equilibration
>
> MD 200ps
> &cntrl
> imin=0,
> irest=1,ntx=7,ntb=0,cut=30,
> ntpr=500,ntwx=500,ntwr=500,
> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> nstlim=100000,dt=.002,ntr=1,
> ntt=1,tempi=300,temp0=300,
> scee=1.2,saltcon=0.1,tol=0.000001,
> icnstph=1,solvph=4,ntcnstph=5
> restraintmask='.CA,C,N,O',restraint_wt=0.5
>
> Production
> MD 2.5ns
> &cntrl
> imin=0,
> irest=1,ntx=7,ntb=0,cut=30,
> ntpr=500,ntwx=500,ntwr=500,
> igb=2,ntc=2,ntf=2,nrespa=1,tautp=2.0,
> nstlim=1250000,dt=.002,
> ntt=1,tempi=300,temp0=300,
> scee=1.2,saltcon=0.1,tol=0.000001,
> icnstph=1,solvph=4,ntcnstph=5
> /
>
> I kept icnstph=0 in consttant protonation.
>
> In a paper i have seen that RMSD for CA is 2.5 angstrom when crystal
> structure
> taken as reference for constant protonation and higher for constant pH for
> 3ns
> run.
>
>
> How i can solve this problem ?
>
>
>
>
> > A single number, i.e. RMSD, is no substitute for actually visualizing
> your
> system. Also keep in mind that 30.0 and even 5.0 are very strong restraint
> force constants, and the system will hardly move at all during these steps.
> Can you see what is happening during the trajectory? Also, did you use the
> same exact protocol when you did the constant protonation simulations? Did
> you use the same force constants? It seems strange that the RMSD for the
> constant protonation was larger in the heating/equilibration for constant
> protonation than it was for constant pH (I think you must have used
> different
> restraints).
> >
> > Finally, what frame are you aligning to? Both should be aligned to the
> same
> structure to get a legitimate comparison.
> >
> > Good luck!
> > Jason
> >
> > On Tue, Jul 27, 2010 at 6:15 AM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >> I have done the constant pH 4 simulation of lysozyme.
> >> 1) I minimized the structure using restraint on backbone atom,
> restraint_wt =
> 30.0
> >> for 3000 steps.
> >> 2) I heat the system gradualy for 1K/1ps using restraint on backbone
> atom,
> restraint_wt = 5.0
> >> 3) Equilibration for 200ps using restraint on backbone atom,
> restraint_wt = 1.0
> >> 4) Production run for 10ns without restraint.
> >> I also did the whole thing using icnstph=0 (constant protonation)to
> compare both
> >> result
> >> I processed the trajectory using ptraj and got the following result:
> Heating
> >> maximum rmsd in const pH MD - 0.98
> >> maximum rmsd in const protonation - 2.1
> >> Equilibration
> >> maximum rmsd in const pH MD - 1.15
> >> maximum rmsd in const protonation - 3.8
> >> Production
> >> maximum rmsd in const pH MD - 5.5 (in 5ns)
> >> maximum rmsd in const pH MD - 10.9 (in next 5ns)
> >> maximum rmsd in const protonation - 5 (in 5ns)
> >> maximum rmsd in const protonation - 6 (in next 5ns)
> >> In constant pH simulation rmsd in not stabilizing but in case of
> constant
> protonation it is slightly stable.
> >> why rmsd is not stabilizing upto 10ns production run can anyone help me.
> Thanks With regard
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jul 28 2010 - 14:00:08 PDT
