we're still not sure what you restrained. did you use the same refc for all
of the remd runs? it isn't clear since you said below it was from the NPT
run- was that the equilibration right before remd, or something else?
why would you get a vacuum bubble? these are all NVT right?
On Sat, Dec 18, 2010 at 11:52 AM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>
> Quoting Jason Swails <jason.swails.gmail.com>:
>
> > The restraint energy is still outrageous, but I'm not quite sure what was
> > happening with your previous simulation without restraints. Since I
> didn't
> > write the hybrid remd code and I've never used it, I don't know how much
> > help I can be of here.
> >
> > However, Dave Case's point was a good one, and you never really answered
> > it. Did you use the same reference structure for each replica? If you
> > didn't, then this will cause your restraint energies to be very high as
> > well.
> I used the same structure from the single npt simulation about 100ns run.
> And I ran a group equilibrium md for all replicas in order to
> equilibrate each replica in each target temperature to avoid a vacuum
> bubble. the final rst files from this step were used to run remd. So
> do you think I have to run a hybrid REMD without running equil MD to
> use the same reference structure? If so, how do I avoid bubble in the
> space?
> Thank you.
> Bongkeun Kim
> >
> > Good luck!
> > Jason
> >
> > On Sat, Dec 18, 2010 at 12:00 AM, Bongkeun Kim <bkim.chem.ucsb.edu>
> wrote:
> >
> >> Hello,
> >>
> >> I applied this patch and used ntr=1 again.
> >> ...........................................................
> >> =================HYBRID REMD: energy calc for exch
> >> 1=================
> >> HYBRID REMD: Stripping waters
> >> wrapping first mol.: 83.13530 0.00000 41.15202
> >> HYBRID REMD: New natom= 4820
> >> HYBRID REMD: Calling force.
> >>
> >> NSTEP = 0 TIME(PS) = 127.600 TEMP(K) = 0.00 PRESS
> >> = 0.0
> >> Etot = 0.0000 EKtot = 0.0000 EPtot =
> >> 116431771.4632
> >> BOND = 22423.0668 ANGLE = 546043.1091 DIHED =
> >> 388.7305
> >> 1-4 NB = 52961.7061 1-4 EEL = 1814.5928 VDWAALS =
> >> -5494.9108
> >> EELEC = -6066.5669 EGB = -3141.0101 RESTRAINT =
> >> 115822842.7455
> >> EAMBER (non-restraint) = 608928.7177
> >> TEMP0 = 501.0000 REPNUM = 32 EXCHANGE# =
> >> 0
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >>
> >> HYBRID REMD: myEptot= ************ myTargetTemp= 501.00
> >> HYBRID REMD: Restoring...
> >> =========================END HYBRID REMD energy
> >> calc.=========================
> >> REMD: myEptot= 116431771.4632 myTargetTemp= 501.00 mytemp= 0.00
> >> ==========================REMD EXCHANGE
> >> CALCULATION==========================
> >> Exch= 1 RREMD= 0
> >> Replica Temp= 501.00 Indx= 32 Rep#= 32 EPot= **********
> >> Partner Temp= 285.10 Indx= 1 Rep#= 1 EPot= **********
> >> Metrop= 0.000000E+00 delta= 0.181951E+04 o_scaling= -1.00
> >> Rand= 0.821770E+00 MyScaling= -1.00 Success= F
> >> ========================END REMD EXCHANGE
> >> CALCULATION========================
> >> REMD: checking to see if bath T has changed: 501.00->501.00
> >> | # of SOLUTE degrees of freedom (RNDFP): 59256.
> >> | # of SOLVENT degrees of freedom (RNDFS): 0.
> >> | NDFMIN = 59256. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> >> 59256.
> >> | TOTAL # of degrees of freedom (RNDF) = 59256.
> >> vlimit exceeded for step 8; vmax = 135.1554
> >> vlimit exceeded for step 10; vmax = 98.9017
> >> ...........................................................
> >>
> >> So, there is only one ****** on HYBRID REMD: myEptot= ************
> >> and EPtot is still large but is not ****. Because EPtot is too large,
> >> I'm afraid that exchanges occur or not.
> >> How do you think this output.
> >> Thank you.
> >> Bongkeun Kim
> >>
> >> Quoting Jason Swails <jason.swails.gmail.com>:
> >>
> >> > Hello,
> >> >
> >> > I think your problem lies in the use of coordinate restraints with
> hybrid
> >> > REMD. One of the steps that hybrid REMD has to do is reimage all of
> the
> >> > water molecules and place it at the location of its closest periodic
> >> image
> >> > since GB methods are inherently non-periodic and know nothing about
> >> > alternate images.
> >> >
> >> > One of the things done in "subroutine stripwat" in remd.f is the
> >> centering
> >> > of the entire system with respect to its center of mass. The reason I
> >> think
> >> > you are having issues is that the coordinates are adjusted by the
> center
> >> of
> >> > mass position, but the reference coordinates are never adjusted.
> >> >
> >> > I'm not positive this will work, but I included a patch which will
> adjust
> >> > the reference coordinates in exactly the same way as the normal
> >> > coordinates. Apply it to the latest, fully patched amber11 from
> >> AMBERHOME.
> >> >
> >> > cd $AMBERHOME
> >> > patch -p0 -N < hybrid_remd.patch
> >> >
> >> > Then recompile. Also please report back whether it worked or not.
> One
> >> > other thing to try that probably should've been mentioned before is
> >> testing
> >> > to see that it worked if you don't include restraints, just to make
> sure
> >> > that it is in fact the restraints that are causing the issue.
> >> >
> >> > Hope this helps,
> >> > Jason
> >> >
> >> > On Fri, Dec 17, 2010 at 11:43 AM, Bongkeun Kim <bkim.chem.ucsb.edu>
> >> wrote:
> >> >
> >> >> Quoting case <case.biomaps.rutgers.edu>:
> >> >>
> >> >> > On Fri, Dec 17, 2010, Bongkeun Kim wrote:
> >> >> >>
> >> >> >> I just run the hybrid remd and checked the output file.
> >> >> >> It said ********** on EPot. Does it mean only the number is too
> big
> >> to
> >> >> >> print or is there any problem on this run?
> >> >> >
> >> >> > There seems to be a problem with the restraint energy:
> >> >> >
> >> >> >> EELEC = -6589.2279 EGB = -3004.6220 RESTRAINT
> >> >> >> =57092146.9150
> >> >> >
> >> >> > You can't run replica exchange simulations with ntr>0 (unless, I
> >> guess,
> >> >> that
> >> >> > all replicas have the same reference structure. Also, be sure that
> >> you
> >> >> can
> >> >> > sucessfully run non-exchange simulations at each temperature of
> >> interest.
> >> >> >
> >> >>
> >> >> I already tried to run it with full explicit water and it gave me no
> >> >> problem. But this run demands too many resources.
> >> >>
> >> >> With hybridgb, EPtot = 58053860.3203 and
> >> >> Without hybbridgb, EPtot = 546283.2545.
> >> >>
> >> >> Also, RESTRAINT = 57444151.6840 with hybridgb and
> >> >> RESTRAINT = 177.4334 without hybridgb.
> >> >> It seems like the hybridgb method overestimates restraint energy of
> my
> >> >> graphite surface too much. I checked the structure of whole system.
> >> >> The peptide lies on the graphite surface now. I think explicitly
> >> >> considered water molecules by numwatkeep=500 are on the other side of
> >> >> graphite surface, that is across the surface. Do you think this makes
> >> >> problems?
> >> >> Thank you.
> >> >> Bongkeun Kim
> >> >>
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Jason M. Swails
> >> > Quantum Theory Project,
> >> > University of Florida
> >> > Ph.D. Graduate Student
> >> > 352-392-4032
> >> >
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 18 2010 - 11:00:04 PST
