Hi,
On Sat, Feb 7, 2015 at 2:22 PM, Hadeer ELHabashy
<hadeer.elhabashi.gmail.com> wrote:
> under ff99 force field . After 117 ns of simulation I thought that the
> protein has reached the equilibrium, However it starts to partially unfold
> after that . That was very obvious and illogical to me because the protein
> tolerated 117 ns of simulation with some favorable and reasonable local
> conformational change and after that starts to unfold. the used protocol is
> included below. Also, The RMSD graph is attached !
Without knowing anything about your system it's tough to say anything
for sure, but your system doesn't seem very stable to me at all. By
~20 ns of simulation time you're already in the 8 Ang. RMSD range,
which increases to above 10 Ang. by ~40 ns. These values are quite
large, and indicate that your system really doesn't look like what it
started as.
> What do you think the reason of this behavior?
> Do you think the old force field of ff99 may be the reason for this ?
It's possible, but there's no way of knowing from just one simulation.
Why are you even using this force field? It's quite old and there are
far better protein FFs available.
> Do think it is an accidental behavior that may not be repeated if I
> re-start the simulation from good earlier restart file?
Nothing here is an "accident". Maybe you experienced a rare unfolding
event. Maybe it will unfold like this every time. You have no
statistics so you can't say anything about the probability of anything
happening in your simulation. Your best bet here (in addition to using
a modern protein FF) may be to look up recent studies which are
similar to what you want to do and see what FFs/protocols/etc they
used.
Hope this helps,
-Dan
> what do you think may be the source of errors in this protocol ?!
>
> 1- 800 steps of minimization round 1 with restrains
>> > &cntrl
>> > imin=1, nmropt=0,
>> > ntx=1, irest=0,
>> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
>> > ntf=2, ntb=1, igb=0, ntc=2, cut=10.0,
>> > maxcyc=800, ncyc=100, ntmin=1,
>> > ibelly=0, ntr=1, restraint_wt=5.0, restraintmask=':1-175',
>> > &end
>>
>> >
>> > 2- heating up to 100 K
>> > &cntrl
>> > imin=0, nmropt=0,
>> > ntx=1, irest=0,
>> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
>> > ntf=2, ntb=2, igb=0, ntc=2, cut=10.0,
>> > nstlim=50000, nscm=500, nrespa=1, dt=0.001,
>> > Tempi=0.0, Temp0=100.0, ntt=3, gamma_ln=2.0,
>> > pres0=1.0, ntp=1, taup=1.0,
>> > ntr=1, restraint_wt=5.0, restraintmask=':1-175',
>> > &end
>>
>> >
>> > 3- 800 steps of minimization round 2 without restrains
>> > &cntrl
>> > imin=1, nmropt=0,
>> > ntx=1, irest=0,
>> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
>> > ntf=2, ntb=1, igb=0, ntc=2, cut=10.0,
>> > maxcyc=800, ncyc=100, ntmin=1,
>> > &end
>> >
>>
>> > 4- heating up to 310 (over 9 rounds each of 50 ps and heating upto 25 K
>> > except the last step) with restrains
>> > &cntrl
>> > imin=0, nmropt=0,
>> > ntx=1, irest=0,
>> > ntxo=1, ntpr=100, ntrx=1, ntwr=100, ntwx=100,
>> > ntf=2, ntb=2, igb=0, ntc=2, cut=10.0,
>> > nstlim=50000, nscm=500, nrespa=1, dt=0.001,
>> > Tempi=100.0 , Temp0=125.0 , ntt=3, gamma_ln=2,
>> > pres0=1.0, ntp=1, taup=0.05,
>> > ntr=1, restraint_wt=5.0, restraintmask=':1-175',
>> > &end
>>
>
>
>> > 5- production MD
>> > &cntrl
>> > imin=0, nmropt=0,
>> > ntx=5, irest=1, ntrx=1,
>> > ntxo=1, ntpr=500, ntwr=500, iwrap=1, ntwx=500,
>> > ntf=2, ntb=2, igb=0, ntc=2, cut=10.0,
>> > nstlim=50000, nscm=500, nrespa=1, dt=0.002,
>> > Tempi=310.0, Temp0=310.0, ntt=3, gamma_ln=2,
>> > pres0=1.0, ntp=1, taup=2.0,
>> > &end
>
>
>
> Best Regards
> Thanks in advance !
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Feb 08 2015 - 16:00:02 PST
