[gmx-users] problem going from cut-off to pme
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
>>>> 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.
>>> 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.
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users