From: Wang, Boyang (bwang9_at_uic.edu)
Date: Tue Jul 24 2007 - 20:43:50 CDT
Hi Peter,
thanks for your help.
Boyang.
On Tue, July 24, 2007 5:54 pm, Peter Freddolino wrote:
> Would you also be willing to send me the logfile from your run? I get
> fairly strong initial electrostatic repulsion when I try this:
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 0.0000 0.0000 0.0000
> 0.0000 107.0143 -0.0352 0.0000
> 0.0000 0.5132 107.4923 86.0785
> 107.4963 107.4963 86.0785 310.7973
> 310.7973 27000.0000 310.7973 310.7973
>
>
> After the first couple hundred steps, though, the electrostatic energy
> does drop to 0 because your atoms are flying apart (look at the dcd). It
> looks like you tried to fix their positions, but the beta and occupancy
> columns of the pdb for fixing them are both 0. You need to either fix
> them, or use long range electrostatics or a longer cutoff, if you expect
> them to continue interacting...
>
> Let me know if this doesn't make sense.
> Peter
>
>
> Wang, Boyang wrote:
>> Hi Peter,
>>
>> thanks.
>>
>> Dear all,
>>
>> when I run the simulation of two charged atoms, I see that the output of
>> electrostatic energy is 0.
>>
>> I am very confused and I appreciate that you would help me with this
>> problem using the attached simulation files.
>>
>>
>> Thanks.
>>
>> Boyang.
>>
>
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