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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