[gmx-users] problem going from cut-off to pme

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 8 20:35:47 CET 2006

Yiannis wrote:
> Well, my initial guess was something wrong with the structure. But  the 
> same gro file gives a correct minimisation with cut-off.
> So I tried a 0 step minimisation to see which component is different.  
> Here it is:
> ==> cutoff.xvg <==
> @ s0 legend "Coulomb (SR)"
>     0.000000  -7838.336914
> ==> pme4.xvg <==
> @ s0 legend "Coulomb (SR)"
> @ s1 legend "Coul. recip."
>     0.000000  -8141383915228874407936.000000  -9205.502930
> Obviously the Coulomb(SR) is aberrant. The only line I changed  between 
> the two mdp is:
> coulombtype              =  cut-off
> to
> coulombtype              = pme
> I don't understand why the Coulomb SR is different and even more why  it 
> is illogical.
> Could it be pme parameters? I keep the defaults (pme=4 or 8 does  change 
> a little the reciprocal component but not the SR).

Possibly. Please give us the .mdp file. You may have only changed 
coulombtype, but there could be other junk there depending where you got 
the original from.

pme_order != 4 is broken in version 3.3, as discussed many times on this 
mailing list. There's a fix to src/mdlib/pme.c on the gromacs ftp site, 
or you can wait for the upcoming 3.3.1 release.

The Coulomb SR would necessarily be different between cut-off and PME. 
Changing only the PME interpolation order necessarily will only change 
the reciprocal-space component. The sum of SR+recip for PME will be 
different from the SR for cut-off. If you don't understand why any of 
these happen, then you need to go and read some basic stuff explaining 
the two methods - the gromacs manual is a good place to start.


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