Alan Dodd wrote:
Interestingly, merging the peptide chains to one
results in PR working fine. Smells like a bug to
me... but I guess that's the price of using an old
version.
We have done PR MD applied on peptides (40) separated
from each other by water molecules and everything went
fine an
Interestingly, merging the peptide chains to one
results in PR working fine. Smells like a bug to
me... but I guess that's the price of using an old
version.
--- Steffen Wolf <[EMAIL PROTECTED]> wrote:
> Yes, so it looks that minimization ended at a
> metastable point, which
> was surmounted by
Interesting idea, but multiple different start points
have failed with PR, and succeeded with normal MD.
Freeze groups seem to be working OK, so I'm using that
for now - after all, it doesn't need to be 'real', I
just want to equilibrate the lipid/solvent without
moving my carefully-placed peptide
Alan Dodd wrote:
No, minimisation was without PR. Surely minimisation
with PR would *increase* bad contacts, rather than
removing them? I've tried running for a while under
normal MD, successfully and without LINCS errors, then
taking the endpoint and running under PR, but it still
crashes almo
No, minimisation was without PR. Surely minimisation
with PR would *increase* bad contacts, rather than
removing them? I've tried running for a while under
normal MD, successfully and without LINCS errors, then
taking the endpoint and running under PR, but it still
crashes almost instantaneously,
Hi Alan,
well, no, position restraints (and your definition) seem to be fine, and
they work well with my protein/membrane system. Sounds more like your
system is still not well minimized. Using the freezegroup option is not
such a good way, because it will not work well together with the
press
Hello,
I'm trying to run position restraints on multiple
peptides in a protein/bilayer/water system. MD
*without* position restraints runs absolutely fine,
but as soon as I stick that "define = -DPOSRES" in,
some of the molecules explode within a matter of fs.
Any idea why this might be? Is MD w
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