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

[Yang Ye]

still the previous advice: check the structure visually. I guess that 
there is bad contact.

Yang Ye

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).
>
> Yiannis
>
>
> 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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>
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