Re: [AMBER] Is this output OK from the hybrid remd?

From: Bongkeun Kim <bkim.chem.ucsb.edu>
Date: Sat, 18 Dec 2010 08:52:39 -0800

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
>> >>
>> >>
>> >>
>> >> _______________________________________________
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>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Graduate Student
>> > 352-392-4032
>> >
>>
>>
>>
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>





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Received on Sat Dec 18 2010 - 09:00:02 PST
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