On Tue, Dec 30, 2014 at 12:46 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
wrote:
> Dear Roitberg and Jason
>
> Thank you for point out my mistake.
>
> Yes it is 99.5% choline lactate and 0.5% water in this system. And I am
> running with different percentage of IL.
>
> For 100% choline lactate system
>
> ------------------------------------------------------------------------------
> A V E R A G E S O V E R 2500000 S T E P S
>
> NSTEP = 2500000 TIME(PS) = 35590.000 TEMP(K) = 297.96 PRESS =
> 1.0
> Etot = 1807.4839 EKtot = 13944.1153 EPtot =
> -12136.6315
> BOND = 5148.9220 ANGLE = 8238.6012 DIHED =
> 4052.6302
> 1-4 NB = 2770.0536 1-4 EEL = 5548.6008 VDWAALS =
> -8363.3905
> EELEC = -29532.0487 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 960.4335 VIRIAL = 957.3126 VOLUME =
> 146678.9676
> Density =
> 1.1201
> Ewald error estimate: 0.2555E-02
>
> ------------------------------------------------------------------------------
>
> For 99.5% choline lactate and 0.5% water system
>
> ------------------------------------------------------------------------------
> A V E R A G E S O V E R 2500000 S T E P S
>
> NSTEP = 2500000 TIME(PS) = 30590.000 TEMP(K) = 297.95 PRESS =
> 1.0
> Etot = 1366.4317 EKtot = 13993.8146 EPtot =
> -12627.3829
> BOND = 5142.8490 ANGLE = 8228.4576 DIHED =
> 4045.2279
> 1-4 NB = 2770.8857 1-4 EEL = 5725.9239 VDWAALS =
> -8217.3621
> EELEC = -30323.3648 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 987.0209 VIRIAL = 983.7836 VOLUME =
> 147776.7168
> Density =
> 1.1175
> Ewald error estimate: 0.2444E-02
>
> ------------------------------------------------------------------------------
>
> For 99% choline lactate and 1.0% water system
>
> ------------------------------------------------------------------------------
> A V E R A G E S O V E R 2500000 S T E P S
>
> NSTEP = 2500000 TIME(PS) = 35590.000 TEMP(K) = 297.95 PRESS =
> 1.0
> Etot = 905.6418 EKtot = 14041.7827 EPtot =
> -13136.1409
> BOND = 5138.6650 ANGLE = 8233.4022 DIHED =
> 4043.5382
> 1-4 NB = 2769.8187 1-4 EEL = 5744.7354 VDWAALS =
> -8111.2161
> EELEC = -30955.0842 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 1012.0545 VIRIAL = 1008.8662 VOLUME =
> 148219.8584
> Density =
> 1.1196
> Ewald error estimate: 0.2371E-02
>
> ------------------------------------------------------------------------------
>
> Please suggest me
>
Then I refer back to my statement that a positive energy does not by
itself indicate a problem (indeed, in your case the potential energy is
actually negative, but the kinetic energy is large enough to make the total
energy positive).
I'd encourage investigation (it will certainly help your own understanding
as well as helping to reveal any problems if they do exist) to see if you
can explain the relative magnitudes of the energy terms there, if you're
concerned about the parameters. You should also make sure your system is
net neutral (I'm not sure if choline lactate carries a net charge or not...)
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 29 2014 - 22:30:02 PST
