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

Yiannis ioannis.nicolis at free.fr
Wed Mar 8 22:27:24 CET 2006

Le 8 mars 06 à 22:22, Mark Abraham a écrit :

> Yiannis wrote:
>> 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).
> Yes, do that as well. In the meantime, your integrator is md which  
> isn't useful for attempting energy minimization.

Of course :-) For minimisations I used steep or l-bfgs. I put md with  
nsteps=0 just to compute the initial energies (I believe that would  
do it also with steep).
I 'll go for the charge groups check and the reading of the sections  
in the manual.


>>> 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.
> Sure.
>>> 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...
> The Ewald beta parameter (controlled indirectly in gromacs through  
> ewald_rtol) changes the relative weight and accuracy of the direct  
> and reciprocal space components in a contrary manner. Sections  
> 4.1.6 and 4.9 of the manual describe this briefly. There will exist  
> a value that gives numerical agreement of SR between PME and Cut- 
> off, but it doesn't mean anything.
> Mark
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