Thomas Piggot wrote:
Whilst this 'problem' you are seeing is probably as Justin has described
(a periodic boundary visualisation effect), you should also beware when
performing carbohydrate/sugar simulations with the default parameters in
the force field files. If I were you I would check the entries against
the published parameters (so Lins et al. if you wish to use the 45A4
sugar parameters). From my experience then there are some mistakes in
the parameters in the force field files.
If this is still the case in the latest release, please file an issue on redmine
so that it can be fixed.
-Justin
Cheers
Tom
nishap.pa...@utoronto.ca wrote:
Thanks Justin!
I am using constraints, but like you said it could be just
PBC. I did compare some of my calculations to experimental values and
they are fairly similar.
Nisha P
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
nishap.pa...@utoronto.ca wrote:
Hello,
I ran a simulation of one molecule of galactose (cyclic) in
water. After the simulation run, when I checked the trajectory file
in VMD, the bonds in the galactose molecule stretched and during
the run changed back to its original starting form. I am using
GROMOS force field ffG53A6 and parameters as mentioned for
carbohydrates in the forcefield, so I am not sure what went wrong.I
generated topology using 'pdb2gmx' command. Also GROMACS did not
give any warning during the run and my simulation did not crash.
Any insights?
You can check bond length distributions with g_bond. Are you using
constraints? Are you sure this isn't just a periodicity artifact
during visualization? If the bonds deviated severely from equilibrium
values or constraint lengths, the simulation would have crashed, so I
suspect that what you're seeing is just PBC.
-Justin
Thanks.
Nisha P
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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