Did you do any minimization or equilibration? If not, it might be good to
read some work in the literature where people do similar things, and follow
their procedures. Something is going wrong early in the simulation and you
are not writing output frequently enough to see what happens.
If you are unsure what is going wrong, isolate variables. For example, try
a lower restraint weight and see if that helps.
On Aug 25, 2016 7:04 AM, "Elisa Pieri" <elisa.pieri90.gmail.com> wrote:
> This is what the RESULTS section looks like:
>
> ------------------------------------------------------------
> --------------------
> 4. RESULTS
> ------------------------------------------------------------
> --------------------
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 11.96 PRESS =
> 0.0
> Etot = -4871.1063 EKtot = 167.1679 EPtot =
> -5038.2742
> BOND = 412.9686 ANGLE = 1179.5946 DIHED =
> 3613.8953
> 1-4 NB = 2442.1380 1-4 EEL = 17099.2356 VDWAALS =
> -896.0282
> EELEC = -26098.6669 EGB = -2791.4112 RESTRAINT =
> 0.0000
> -----------------------------------------------------------
> -------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ============================================================
> ===================
>
> NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = NaN PRESS =
> 0.0
> Etot = NaN EKtot = NaN EPtot =
> **************
> BOND = ************** ANGLE = 547405.9274 DIHED =
> 19855.8962
> 1-4 NB = 0.0000 1-4 EEL = 0.2489 VDWAALS =
> 0.0000
> EELEC = 997.3637 EGB = -66293.8715 RESTRAINT =
> 289530816.0772
> EAMBER (non-restraint) = **************
> -----------------------------------------------------------
> -------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ============================================================
> ===================
>
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = NaN PRESS =
> 0.0
> Etot = NaN EKtot = NaN EPtot =
> **************
> BOND = ************** ANGLE = 638733.4240 DIHED =
> 19778.0610
> 1-4 NB = 0.0000 1-4 EEL = 0.2033 VDWAALS =
> -0.0000
> EELEC = 1464.2886 EGB = -66287.9607 RESTRAINT =
> **************
> EAMBER (non-restraint) = **************
> -----------------------------------------------------------
> -------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ============================================================
> ===================
>
> NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = NaN PRESS =
> 0.0
> Etot = NaN EKtot = NaN EPtot =
> **************
> BOND = ************** ANGLE = 763432.0545 DIHED =
> 19913.0211
> 1-4 NB = 0.0000 1-4 EEL = 0.3792 VDWAALS =
> -0.0009
> EELEC = 1296.2820 EGB = -64197.0815 RESTRAINT =
> **************
> EAMBER (non-restraint) = **************
> -----------------------------------------------------------
> -------------------
>
>
> I set such a high restraint weight because I need the protein to be as
> freezed as possible, allowing only a cavity to move (as silly as it can
> sound). Is there a better way of doing it?
>
> On Thu, Aug 25, 2016 at 11:41 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > What do you see in the .out file? You may have to print each step. Look
> > for energies going to infinity and note which atom GMAX is on when that
> > occurs, then I'd visualize your trajectory to see if there is a specific
> > problem in that region. Your restraint weight seems high - you might try
> > reducing it to 1 or .1, but I don't have experience with that.
> >
> > Bill
> >
> >
> > On 8/25/16 2:12 AM, Elisa Pieri wrote:
> > > Hi,
> > >
> > > I heated a protein starting from a good rst7 file using this input:
> > >
> > > &cntrl
> > > imin=0, irest=0, ntx=1,
> > > ntpr=500, ntwx=500, nstlim=1000000,
> > > dt=0.002, ntt=3, tempi=10,
> > > temp0=300, tautp=2.0, ig=-1,
> > > ntp=0, ntc=2, ntf=2, cut=999,
> > > ntb=0, igb=2, tol=0.000001,
> > > nrespa=1, saltcon=0.1, ntxo=1,
> > > gamma_ln=5.0, ntwr=500, ioutfm=1,
> > > nmropt=1, ntr=1, restraint_wt=40.0,
> > >
> > > restraintmask='!:86,113,114,117,118,121,122,125,167,181,
> > 186-189,191,207,208,211,212,261,265,268,269,272,292,295,296,298',
> > > /
> > > &wt
> > > TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
> > > VALUE1=10.0, VALUE2=300.0,
> > > /
> > > &wt TYPE='END' /
> > >
> > > The rst7 file that I get at the end is this (first lines):
> > > default_name
> > > 5649 0.2000000E+04
> > > 29.1820225 30.7497409 -22.1838690*******************
> > *****************
> > > ************************************************************
> ************
> > > ************************************************************
> ************
> > > ************ 12.7407017********************
> ****************************
> > > ************************************************
> 12.7410547************
> > > ************************************************************
> ************
> > > ************************************ 94.9745896************
> -33.0591310
> > > ************************************************************
> ************
> > > ************************************************************
> ************
> > > 3655.05540903568.3796548 -33.9095279*******************
> *****************
> > > ************************************************************
> ************
> > > ************************************************************
> ************
> > > ************************************************************
> ************
> > > ************5190.95423225142.85060162143.2519731***********
> *************
> > > 3232.4049918************************************************
> ************
> > > ************************************************3535.
> 02488733786.9319069
> > > 4008.1078513************************************************
> ************
> > > ************************************************************
> ************
> > >
> > > What happened? Can somebody help me?
> > >
> > > Thanks!
> > > Elisa
> > > _______________________________________________
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> >
> >
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Received on Thu Aug 25 2016 - 05:00:02 PDT
