> Hi,
>
> Could you please provide your starting coordinate, topology, reference
> coordinate, and input files so I can attempt to reproduce this error?
> As far as I can tell the code is sound. You can send it directly to my
> email address.
>
> Also, there are certain aspects of your system that may be cause for concern:
>
> On Wed, Dec 22, 2010 at 2:21 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>> HYBRID REMD: New natom= 4820
>> HYBRID REMD: New ref natom= 4820
>> HYBRID REMD: Calling force.
>>
>> NSTEP = 0 TIME(PS) = 124.600 TEMP(K) = 0.00
>> PRESS = 0.0
>> Etot = 0.0000 EKtot = 0.0000 EPtot =
>> 18358499.0386
>> BOND = 21452.3217 ANGLE = 545232.3866 DIHED = 337.2216
>> 1-4 NB = 52797.7673 1-4 EEL = 1810.9335 VDWAALS = -5472.0897
>> EELEC = -6564.7773 EGB = -3058.1446 RESTRAINT =
>> 17751963.4196
>> EAMBER (non-restraint) = 606535.6191
>> TEMP0 = 285.1000 REPNUM = 1 EXCHANGE# = 0
>
> Although your restraint energy is large, your energy without the
> restraints is quite large as well. The angle term in particular seems
> to contribute ~80% to the overall energy, which is not usual,
> especially in a system with only 4820 atoms.
>
> One thing you may want to try is to specify restraints using the
> restraintmask namelist variable instead of using GROUP input. Based on
> the input you initially provided you would want to add something like
> restraintmask=':1-1346' and restraint_wt=1.0 to your input. It may not
> matter but it's certainly worth a try.
>
> -Dan
>
I tested it again with restraintmask=':1-1346' and restraint_wt=1.0
and it did not change the output following.
Thanks.
Bongkeun Kim
\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
=================HYBRID REMD: energy calc for exch 1=================
HYBRID REMD: Stripping waters
wrapping first mol.: 83.13530 0.00000 41.15202
wrapping first mol.: 83.13530 81.46523 41.15202
HYBRID REMD: New natom= 4820
HYBRID REMD: New ref natom= 4820
HYBRID REMD: Calling force.
NSTEP = 0 TIME(PS) = 124.600 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
18358499.0386
BOND = 21452.3217 ANGLE = 545232.3866 DIHED =
337.2216
1-4 NB = 52797.7673 1-4 EEL = 1810.9335 VDWAALS =
-5472.0897
EELEC = -6564.7773 EGB = -3058.1446 RESTRAINT =
17751963.4196
EAMBER (non-restraint) = 606535.6191
TEMP0 = 285.1000 REPNUM = 1 EXCHANGE# =
0
------------------------------------------------------------------------------
HYBRID REMD: myEptot= 18358499.0386 myTargetTemp= 285.10
HYBRID REMD: Restoring...
=========================END HYBRID REMD energy calc.=========================
REMD: myEptot= 18358499.0386 myTargetTemp= 285.10 mytemp= 0.00
==========================REMD EXCHANGE CALCULATION==========================
Exch= 1 RREMD= 0
Replica Temp= 285.10 Indx= 1 Rep#= 1 EPot= **********
Partner Temp= 501.00 Indx= 32 Rep#= 32 EPot= **********
Not controlling exchange.
Rand= 0.248191E+00 MyScaling= 1.33 Success= T
========================END REMD EXCHANGE CALCULATION========================
REMD: checking to see if bath T has changed: 285.10->501.00
REMD: scaling velocities by 1.326 to match new bath T 501.000
| # 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.
\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
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Received on Wed Dec 22 2010 - 13:30:04 PST
