Dear Sir
wish you are fine !
I am running a MDS protocol on a protein in a water box expecting some
conformational changes. I've got some favorable conformation changes
started with starting the simulation and continues until 100 ns of
simulation and beyond . with the following 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,
iwrap=0, ntwx=100, ntwv=0, ntwe=0,
ioutfm=0, ntwprt=0, idecomp=0,
ntf=2, ntb=1, igb=0, nsnb=1,
ipol=0, gbsa=0, iesp=0,
dielc=1.0, cut=10.0, intdiel=1.0,
maxcyc=800, ncyc=100, ntmin=1,
dx0=0.0010, drms=0.00010,
nstlim=0, nscm=2, nrespa=1,
t=0.0, dt=0.001, vlimit=20.0,
ntc=2, jfastw=0, tol=0.00001,
Tempi=0.0, Temp0=0.0, ntt=1, tautp=0.5,
ntp=0, taup=1.0,
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,
iwrap=0, ntwx=100, ntwv=0, ntwe=0,
ioutfm=0, ntwprt=0, idecomp=0,
ntf=2, ntb=2, igb=0, nsnb=1,
ipol=0, gbsa=0, iesp=0,
dielc=1.0, cut=10.0, intdiel=1.0,
nstlim=50000, nscm=2, nrespa=1,
t=0.0, dt=0.001, vlimit=20.0,
ntc=2, jfastw=0, tol=0.00001,
Tempi=0.0, Temp0=100.0, ntt=3, tautp=0.5, gamma_ln=2.0,
pres0=1.0, ntp=1, taup=1.0,
ibelly=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,
iwrap=0, ntwx=100, ntwv=0, ntwe=0,
ioutfm=0, ntwprt=0, idecomp=0,
ntf=2, ntb=1, igb=0, nsnb=1,
ipol=0, gbsa=0, iesp=0,
dielc=1.0, cut=10.0, intdiel=1.0,
maxcyc=800, ncyc=100, ntmin=1,
dx0=0.0010, drms=0.00010,
nstlim=0, nscm=2, nrespa=1,
t=0.0, dt=0.001, vlimit=20.0,
ntc=2, jfastw=0, tol=0.00001,
Tempi=100.0, Temp0=100.0, ntt=1, tautp=0.5,
ntp=0, taup=1.0,
ibelly=0, ntr=0,
&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, ntrx=1,
ntxo=1, ntpr=100, ntrx=1, ntwr=100,
iwrap=0, ntwx=100, ntwv=0, ntwe=0,
ioutfm=0, ntwprt=0, idecomp=0,
ntf=2, ntb=2, igb=0,
ipol=0, gbsa=0, iesp=0,
dielc=1.0, cut=10.0, intdiel=1.0,
nstlim=50000, nscm=2, nrespa=1,
t=0.0, dt=0.001, vlimit=20.0,
ntc=2, jfastw=0, tol=0.00001,
Tempi=100.0 , Temp0=125.0 , ntt=3, tautp=0.01, gamma_ln=2,
pres0=1.0, ntp=1, taup=0.05,
ibelly=0, 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, ntwv=0, ntwe=0,
ioutfm=0, ntwprt=0, idecomp=0,
ntf=2, ntb=2, igb=0,
ipol=0, gbsa=0, iesp=0,
dielc=1.0, cut=10.0, intdiel=1.0,
ibelly=0, ntr=0,
nstlim=50000, nscm=500, nrespa=1,
t=0.0, dt=0.002, vlimit=20.0,
ntc=2, jfastw=0, tol=0.00001,
Tempi=310.0, Temp0=310.0, ntt=3, tautp=0.5, gamma_ln=2,
pres0=1.0, ntp=1, taup=2.0,
&end
The question now : depending on the mentioned protocol
can you see any failure in the pervious protocol ?
can I consider these changes in protein conformation as real time events ?
what are the parameters of the MD control file that can decelerate or
accelerate a real time event ?
does the applied shake ,providing that all the bond interaction involving
hydrogen bonding are omitted, affect the real time event ?
Best Regards
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Received on Thu Feb 05 2015 - 04:00:02 PST
