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

From: Bongkeun Kim <bkim.chem.ucsb.edu>
Date: Fri, 17 Dec 2010 21:00:14 -0800

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
>





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Received on Fri Dec 17 2010 - 21:30:04 PST
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