Thank you all for your replies. I am replying bit delayed as i had to run
few simulations.
I took a DNA molecule (2jpz) from pdb. Then i minimized the structure with
the following input.
STEP 1:
&cntrl
imin=1,ntpr=100, maxcyc=1000,ncyc=700,cut=12,nsnb=10,
ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
/
Then i heated the system and equilibrated with the following inputs, where i
faced the problem of temperature rising to high values (around 3000 K).
STEP 2 and STEP 3
&cntrl
imin=0,ntx=1,irest=0,ntpr=100,ntwr=500,ntwx=500,nstlim=20000,dt=0.001,tempi=100.0,temp0=300.0,
ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=25,restraintmask=':1-22',
ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1, rgbmax=15
/
&cntrl
imin=0,ntx=5,irest=1,ntpr=100,ntwr=500,ntwx=500,nstlim=100000,dt=0.001,tempi=300.0,temp0=300.0,
ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=10,restraintmask=':1-22',
ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
/
I was suggested by amber experts that the problem could be due to
small *cutoff,
restraints or rgbmax*. I used low cut of 12A as it is shown in the DNA
tutorial (section 2) that cut off has less significance when DNA is
simulated with implicit solvation.
Then i did repeated the heating and equilibration phase *without setting the
rgbmax* and with different cutoff and restraints, temperature regulation
keeping the other conditions same.
A: cut=16, restraint = 25, ntt = 3, gamma_ln = 1
: cut= 16, restraint = 5, ntt=3, gamma_ ln = 1
: cut= 16, restraint =0 , ntt=3, gamma_ ln = 1
B: cut=999, restraint = 25, ntt = 3, gamma_ln = 1
: cut= 999, restraint = 5, ntt=3, gamma_ ln = 1
: cut= 999, restraint =0 , ntt=3, gamma_ ln = 1
C: cut=16, restraint = 25, ntt = 1, tautp = 0.5
:cut=16, restraint = 5, ntt = 1, tautp = 0.5
:cut=16, restraint = 0, ntt = 1, tautp = 0.5
D: cut=999, restraint = 25, ntt = 1, tautp = 0.5
:cut=999, restraint = 5, ntt = 1, tautp = 0.5
: cut=999, restraint =0, ntt = 1, tautp = 0.5
I hve attached two pdf's. a.pdf (temperature Vs time), b.pdf (rmsd Vs time)
1) The plot of temp Vs time (a.pdf) shows that, when i use ntt=3 and
gamma_ln =1, the fluctuation in temperature goes down as i reduce the
restraint from 25 to 5 to 0. But when i use ntt=1, tautp=0.5, there is no
wild fluctuations in the temp and it seems that the restraint dosent have
any effect.
What could be the reason for the same ?
Is it wise to conclude that ntt=1 works better with igb=1 ?
When i compare the rmsd (attached b.pdf) from the starting structure, it
seems that the rmsd roughly stays around 2.5A in all the above simulations.
kindly write me how ntt and igb are interrelated ?
2) It would be helpful if you someone suggests me how better i can do the
heating and equilibration with implicit solvation.
Thank in advance,
Bala
On Tue, Mar 17, 2009 at 5:58 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it may be useful to NOT restrain the hydrogens, depending on how you
> built the initial structure.
>
>
> On Tue, Mar 17, 2009 at 12:53 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> > Hi Bala,
> >
> >> *3.in*
> >> &cntrl
> >>
> >>
> imin=0,ntx=1,irest=0,ntpr=100,ntwr=500,ntwx=500,nstlim=20000,dt=0.001,temp
> >> i=100.0,temp0=300.0,
> >> tautp=0.5,
> >>
> >>
> ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=25,r
> >> estraintmask=':1-22',
> >> ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
> >> /
> >
> > tautp will be ignored when ntt=3. A restraint_wt of 25 is pretty high for
> > MD. Something like 5 would probably be better. If your initial structure
> is
> > strained you might find that a lot of potential energy is quickly dumped
> > into the springs as kinetic energy which might take a while to
> equilibrate
> > out.
> >
> > You also don't say how many atoms you have here. The less atoms you have
> the
> > more noise there will be on the kinetic energy and thus temperature.
> >
> > Cut=12 is probably way too small for GB and is leading to a net heating
> of
> > your system that the thermostat doesn't keep up with. Hence your
> temperature
> > is always above the target temperature. Ideally with GB you should not
> use a
> > cut off - set cut=999.0, or at the very least make it 18.0 or more.
> Although
> > from the *'s in your output below I think you have more immediate
> problems
> > than just the cut off.
> >
> >> *5.out*
> >> A V E R A G E S O V E R 100000 S T E P S
> >> NSTEP = 100000 TIME(PS) = 220.000 TEMP(K) = 340.17 PRESS =
> >> 0.0
> >
> >> *6.out* A V E R A G E S O V E R 100000 S T E P S
> >> NSTEP = 100000 TIME(PS) = 320.000 TEMP(K) =********* PRESS =
> >> 0.0
> >> Etot = NaN EKtot = 3568123.6676 EPtot = NaN
> >> BOND = 851450.1246 ANGLE = 15111.5468 DIHED =
> >> 1984.8352
> >> 1-4 NB = 1179.4403 1-4 EEL = -2064.5821 VDWAALS =
> >> 155.2364
> >> EELEC = 404.5486 EGB = NaN RESTRAINT =
> >> 639525195.9927
> >> ESURF= 28.9927
> >> EAMBER (non-restraint) = NaN
> >
> > Your system has blown up. This can be from a combination of things
> although
> > often occurs because your starting structure was highly strained. The
> tough
> > restraints you used were probably sufficient to hold it together but as
> you
> > relaxed them the strained system just flew apart. I suggest you very
> > carefully look at the trajectory files produced and see if you can see
> what
> > causes the system to blow up. Note your bond energy in 6.out above is
> VERY
> > high. You can also try running with ntwx=1 or 5 or so this will allow you
> to
> > watch how things blow up. I suspect the problem started to occur from the
> > very beginning so you should look carefully there. Also rerun step 6 with
> > ntwx=1 and watch what happens.
> >
> > Good luck,
> > Ross
> >
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> > be read every day, and should not be used for urgent or sensitive issues.
> >
> >
> >
> >
> >
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- application/pdf attachment: a.pdf
- application/pdf attachment: b.pdf
Received on Fri Mar 20 2009 - 01:14:35 PDT
