Because 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.
This is the link -
http://www3.interscience.wiley.com/journal/109700491/abstract
I have seen the trajectory both N and C terminus are flying.
I have also fixed all bugs during installation.
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed Jul 28 2010 - 21:30:03 PDT
