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

Yiannis ioannis.nicolis at free.fr
Wed Mar 8 21:33:45 CET 2006

Le 8 mars 06 à 20:35, Mark Abraham a écrit :

> 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.

OK, I attach it to the mail. I got it from somebody who asks me what  
to do and I told him I'll ask the list. Something else I wanted to  
check is the charge groups as it is a zwiterionic molecule (and the  
contacts as Yang Ye suggests).

> 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.

I missed that info, thanks. Anyway, it was set to pme=4, the pme=8  
was just a test.

> 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.

I will do some reading as I understand the second and third assesment  
but not the first one...

> Mark



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