On 4/26/12 11:37 AM, Delmotte, Antoine wrote:
Dear Justin,
Many thanks for your response. I managed to reduce the number of errors by
trying other atom types, by looking at what seemed most likely to be right from
the ffnonbonded.itp and ffbonded.itp files.
Unfortunately, I did not manage to find a combination that both made some sense,
and allowed to remove the errors. So I guess these things need to be
parametrized, as you said.
Could you possibly let me know if there is a relatively easy and straightforward
way to find these parameters? (I guess the answer is probably "no", but it's
always worth asking, I guess...)
You can make a first effort by assigning parameters based on existing, similar,
parameters. They may or may not exist.
I also noticed that there is a option "-zero" in grompp which "Sets parameters
for bonded interactions without defaults to zero instead of generating an
error".
What does it mean exactly? Is it just taking the angles and distances inferred
from the structure as the ones at equilibrium? Is it safe to use it?
What it means is "ignore the problem and simply assign the value of zero for
equilibrium lengths, force constants, etc."
I am just a beginner with MD, and I just want to do a quick run to test
something. I have no need for super high accuracy, and the run I want to try
will be very small (maybe 1 or 2 ns, or something like that), and for a very
large system (~80 000 atoms). Would that be unreasonable to use that "-zero"
option (it is tempting, I must say...)?
I say that using -zero is a bad idea. It ignores the problem and whatever
results you obtain would be questionable, at best. Parameterization of novel
species is an advanced topic. Most people will spend several months developing
good parameters for a new residue or molecule.
-Justin
--
========================================
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
========================================
--
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
