[gmx-users] pme in gmx

Fan Hao f.Hao at chem.rug.nl
Mon Jul 14 03:41:01 CEST 2003

Hi, All:
	I have some basic questions about realization of pme in
Gromacs3.0 especially the electrostatic part. I searched the mailing list
but I could not find specific answers so I raise them here. Any hints will
be sincerely welcome!

1) the way of pme realization in gmx: I assume that the do_fnbf()
did the calculation of direct space inside the rlist/rcoul with the 
formula: 1/r - erf/r which was used in table function of the inner loop
if you set electrostatic type to be PME; the do_pme() did the 
calculation of k space; the do_ewaldlrcorrection() exclude the bound
interaction for direct space inside the rlist/rcoul.
Do I have mistakes in my assumption?

2) I think there is no switch or shift function used in PME around the 
rlist/rcoul, is it?

3) Are there any difference in PME realization between different versions
of gmx, eg. 3.0.5, 3.1.4...? 

Best regards

Yours sincerely

Hao Fan :-)

Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands

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