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From: Carlos Simmerling <carlos.simmerling.gmail.com>

Date: Mon, 13 Jun 2011 09:19:29 -0400

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

Date: Mon, 13 Jun 2011 09:19:29 -0400

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:

_______________________________________________

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AMBER.ambermd.org

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Received on Mon Jun 13 2011 - 06:30:02 PDT

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