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

Yiannis ioannis.nicolis at free.fr
Wed Mar 8 20:15:47 CET 2006

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


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).


Le 8 mars 06 à 07:14, Mark Abraham a écrit :

> Yiannis wrote:
>> Hello,
>> I have a strange problem with a 100 molecule system where I used  
>> cut- off electrostatics and I want to use pme from now.
>> After md with Coulomb cut-off, I minimised with steep (and the  
>> same  Coulomb cut-off) and it ends OK:
>> I take this minimised .gro and I minimise it again but now I  
>> change  to PME electrostatics. It crashes from the beginning with  
>> an infinite  force (not on the atom with the previous maximum  
>> force) and the  energy is huge: 6.56504e+19 instead of -5.0425977e 
>> +04 which was the  end of the previous minimisation. Do you have  
>> any explanation? Should  I change some PME parameters?
> This suggests you are doing something grossly wrong. Check your  
> structures visually, check you're actually feeding in the structure  
> you think you are, check your .mdp file contains what you think it  
> does.
> Mark
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