On Wed, Apr 9, 2014 at 2:19 PM, Christopher A Thiebaut
<cthieba.purdue.edu>wrote:
> My system:
> 4713 protein atoms
> 14925 water molecules
> Bonds to hydrogen constrained in protein
> Rigid (TIP3P water)
>
> Data previously given to temperature selector:
> 5000 protein atoms
> 15000 water molecules
> Bonds to hydrogen constrained in protein
> Rigid water.
> Desired acceptance rate .22
> Low temp 270 K
> High temp 310 K
>
> Temperature ladder for what was entered previously:
> 270.00, 271.24, 272.48, 273.72, 274.97, 276.23, 277.49, 278.75, 280.02,
> 281.30, 282.58, 283.86, 285.15, 286.44, 287.74, 289.04, 290.35, 291.66,
> 292.98, 294.30, 295.62, 296.95, 298.29, 299.63, 300.98, 302.33, 303.68,
> 305.04, 306.41, 307.78, 309.15, 310.53
> (102433 predicted degrees of freedom)
> Temperature ladder from entering correct data:
> 270.00, 271.24, 272.49, 273.74, 275.00, 276.26, 277.52, 278.79, 280.07,
> 281.34, 282.63, 283.92, 285.21, 286.51, 287.81, 289.12, 290.43, 291.75,
> 293.07, 294.39, 295.72, 297.06, 298.40, 299.74, 301.09, 302.45, 303.81,
> 305.17, 306.54, 307.86, 309.23, 310.62
> (101269 predicted degrees of freedom)
>
> Does it seem plausible that this is the cause of the issues? There
> doesn't seem to be much of a difference between these temperature
> distribution.
>
What happens if you try it? What input file are you using?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 09 2014 - 11:30:04 PDT
