I'm not sure what the concern is, can you clarify?
On Apr 9, 2013 10:00 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
> I am trying to follow the protocols in
> http://ambermd.org/tutorials/basic/tutorial3 to obtain some conformational
> sampling for a small peptide of my interest. It turns out that during the
> heating stages (~250K), the total energy of the system becomes +ve. I am
> heating
> it upto 310K and I have pasted below the snapshots from the last heating
> run. I
> am following the protocol in the tutorial.
>
> NSTEP = 39950 TIME(PS) = 49.975 TEMP(K) = 310.94 PRESS =
> 0.0
> Etot = 221.9592 EKtot = 457.8622 EPtot =
> -235.9030
> BOND = 122.9774 ANGLE = 355.1161 DIHED =
> 464.4054
> 1-4 NB = 122.0431 1-4 EEL = 1446.9111 VDWAALS =
> -166.7690
> EELEC = -2024.7384 EGB = -555.8486 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
>
>
> KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
>
> Translational and rotational motion removed
>
> KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
>
> NSTEP = 40000 TIME(PS) = 50.000 TEMP(K) = 306.34 PRESS =
> 0.0
> Etot = 222.0932 EKtot = 451.0901 EPtot =
> -228.9969
> BOND = 116.2790 ANGLE = 351.3472 DIHED =
> 469.2875
> 1-4 NB = 118.3938 1-4 EEL = 1474.4917 VDWAALS =
> -165.3935
> EELEC = -2042.9887 EGB = -550.4139 RESTRAINT =
> 0.0000
>
> ------------------------------------------------------------------------------
> Any comments would be greatly appreciated.
>
> Many thanks and Best Regards,
> Moitrayee
>
>
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Received on Tue Apr 09 2013 - 20:00:02 PDT
