thanks justin for clearing up these issues ..
Am 28.02.2012 15:50, schrieb Justin A. Lemkul:
Vedat Durmaz wrote:
actually, as far as i know, the -DFLEXIBLE argument has no effect
on simulations without explicit water ?!
The #ifdef FLEXIBLE block does only affect explicit water, unless the
topology is somehow modified to use this type of term (probably not).
It shouldn't be used for MD anyway, as all water models were
parameterized to be rigid.
i just copied the "define" line from my explicit simulation systems
.. so, the only define value, that has a meaning is -DPOSRESHELIX.
i didn't use constraints for the first time in my life since implicit
solvent simulations incorporate a much smaller number of atoms and
are therefore not that expensive computationally. i always use this
setting for my explicit simulations only in order to increase the
step size to 2fs with a clear conscience ...
One should also consider the representation of the physical model. It
can be argued that rigid bonds are a more realistic representation of
ground state bonds, in addition to making the simulations more efficient.
-Justin
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
