Hi-
Jason is right about this, but a bigger issue may be that your temperatures
are very high.
You need to consider these things (among others):
- is your time step small enough for stable MD at such a high T?
- are you using restraints to avoid undesired transitions that are facile at
this T (such as chirality inversions, cis/trans isomerization, and more)?
- are you aware that many processes are non-Arrhenius, and using such a high
T can actually slow down REMD convergence? (see work by Ron Levy and others
on this)
On Mon, Jun 13, 2011 at 12:25 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> The problem is that the temperature in this instance is printed with the
> format statement "f6.2", meaning that the range of temperatures that can be
> printed are -99.99 to 999.99 (because only 6 characters are allowed, and 2
> must be decimals).
>
> *End technical, unnecessary explanation*
>
> This doesn't matter at all. Furthermore, all of the temperatures are
> printed in the remlog file (from -999999.99 to 9999999.99 K), so all of the
> REMD printout in the mdout files are superfluous. If you want to get rid
> of
> the ***s, though, you can change the line
>
> write(6,'(a16,a7,f6.2,2(a7,i2),a7,f10.2)') &
>
> to
>
> write(6,'(a16,a7,f8.2,2(a7,i2),a7,f10.2)') &
>
> in $AMBERHOME/src/sander/remd.f
>
> HTH,
> Jason
>
> On Sun, Jun 12, 2011 at 7:16 PM, <tdo.chem.ucsb.edu> wrote:
>
> > Hi,
> >
> > I am running REMD in vacuum (max temp is about 2100K). Everything is
> > running fine except when I read the mdout files, I see that all high
> > temperatures (above 1000K) are shown as temp=******.
> >
> >
> >
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> >
> --------------------------------------------------------------------------------
> >
> > REMD: Getting initial energy for replica 33
> > | # of SOLUTE degrees of freedom (RNDFP): 1622.
> > | # of SOLVENT degrees of freedom (RNDFS): 0.
> > | NDFMIN = 1622. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> > 1622.
> > | TOTAL # of degrees of freedom (RNDF) = 1622.
> > ---------------------------------------------------
> >
> > eedmeth=4: Setting switch to one everywhere
> >
> > ---------------------------------------------------
> > | Local SIZE OF NONBOND LIST = 107029
> > | TOTAL SIZE OF NONBOND LIST = 209287
> >
> > NSTEP = 0 TIME(PS) = 292500.000 TEMP(K) = 1559.38 PRESS
> > = 0.0
> > Etot = 4058.5830 EKtot = 2513.1176 EPtot =
> > 1545.4654
> > BOND = 528.8743 ANGLE = 1445.6975 DIHED =
> > 555.8678
> > 1-4 NB = 205.8017 1-4 EEL = 2189.8266 VDWAALS =
> > -62.2561
> > EELEC = -3318.3462 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > TEMP0 = 1511.0900 REPNUM = 33 EXCHANGE# =
> > 0
> >
> >
> >
> ------------------------------------------------------------------------------
> >
> > REMD: Exiting runmd after getting initial energies for replica 33
> > REMD: myEptot= 1545.4654 myTargetTemp= ****** mytemp= 0.00
> > ==========================REMD EXCHANGE
> > CALCULATION==========================
> > Exch= 1 RREMD= 0
> > Replica Temp= ****** Indx= 33 Rep#= 33 EPot= 1545.47
> > Partner Temp= ****** Indx= 32 Rep#= 32 EPot= 1429.83
> > Not controlling exchange.
> > Rand= 0.716490E+00 MyScaling= -1.00 Success= F
> > ========================END REMD EXCHANGE
> > CALCULATION========================
> > REMD: checking to see if bath T has changed: ******->******
> > | # of SOLUTE degrees of freedom (RNDFP): 1622.
> > | # of SOLVENT degrees of freedom (RNDFS): 0.
> > | NDFMIN = 1622. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> > 1622.
> > | TOTAL # of degrees of freedom (RNDF) = 1622.
> > | RE_POSITION Moving by 0.901579 1.226505 0.728351
> > | RE_POSITION Moving by -0.007677 0.427082 0.040594
> > | RE_POSITION Moving by 0.065916 0.149577 0.172735
> > | RE_POSITION Moving by -0.024492 -0.135742 -0.573912
> > | RE_POSITION Moving by -0.116004 -0.520011 0.580946
> > | RE_POSITION Moving by 0.380212 -0.148886 -1.527626
> > REMD: myEptot= 1539.5586 myTargetTemp= ****** mytemp= ******
> >
> > Other output files (mdcrd files, restart files) look normal, so I
> > expect there is a problem with the output digit for temperature. A
> > friend suggested me to edit the remd.f file in src/sander/, but I am
> > not sure about what to do.
> >
> > Thank you,
> >
> >
> >
> > --
> > Thanh D. Do
> > Department of Chemistry & Biochemistry
> > University of California Santa Barbara
> > Santa Barbara, California, 93106
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 13 2011 - 06:30:02 PDT
