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.
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
