Ionic liquids

Dear Lammps users,

I am a new user of Lammps and intend to use it to model room temperature ionic liquids (RTILs) in the presence of a thermal gradient. I have chosen Lammps for this purpose as I am aware that it has some of the best capabilities for modelling temperature gradients.

After reading over the basics of the Lammps manual it seems that making data files for complex systems such as RTILs is non-trivial and that since the topology file of programs such as Gromacs is replaced with an input file, this too is not simple.

I was hoping that someone could point me in the right direction to either obtain a means of constructing a data file, or might even have a ready-made data files for such a system. Any help would be enormously appreciated!

Many thanks, James.

James,

Dear Lammps users,

I am a new user of Lammps and intend to use it to model room temperature
ionic liquids (RTILs) in the presence of a thermal gradient. I have chosen
Lammps for this purpose as I am aware that it has some of the best
capabilities for modelling temperature gradients.

Not sure what you mean with the above statement. A temp gradient can
be modeled by
simply setting two regions within your simulation box at different
temperatures via thermostats.
Are you sure you can't do that with the other code you are more familiar with?

After reading over the basics of the Lammps manual it seems that making data
files for complex systems such as RTILs is non-trivial and that since the
topology file of programs such as Gromacs is replaced with an input file,
this too is not simple.

Lammps is a rich framework that allows you to do many things on
atomistic systems.
Yet, it does not the bookkeeping for you. You (the user) are the only
one to be blamed
if the interaction coefficients between the atoms in your simulations
are defined incorrectly.
This can be seen as a limitation but also as a strength 'cause it
gives you more freedom/power.
As to the simplicity issue, if you can't make an input file perhaps
you should start wondering
why are you trying to get into the atomistic simulations field. Making
the input file will not be
the only hurdle to be faced...

I was hoping that someone could point me in the right direction to either
obtain a means of constructing a data file, or might even have a ready-made
data files for such a system. Any help would be enormously appreciated!

And here you have identified an avenue (actually, I did) that could
make the Lammps
community even wider while pushing forward science at a faster pace.
Wouldn't be nice
to have a comprehensive database of well-tested Lammps input scripts
that tackle real life
research situations!!! Developing content could be as profitable as
developing software...
For the time being, you'll have to rely on the goodwill of any other
user who might have used
Lammps to simulate the IL you are after. Which one BTW?
Carlos

Wouldn't be nice
to have a comprehensive database of well-tested Lammps input scripts
that tackle real life
research situations!!!

That would be great and we'd support whoever wants to work
on it, whether on their own site or if someone wants to
"own" it on the LAMMPS WWW site.

We tried adding this page to the LAMMPS WWW site
http://lammps.sandia.gov/scripts.html
but it gets almost zero contributions.

Steve

I am aware of your site but I think It doesn't appeal to people
because the interface is poor and you guys
didn't try to "milk" the "ultimate currency" that maters to science
people, i.e, citations. Have some ideas but in a nutshell, if you had
designed a CMS-type site (pretty) where people could link their
scripts to published papers, add comments, etc I think it would have
better chances of taking off. You might have to gather an initial
critical mass of input scripts though. By just looking at the
statistics, the majority of the requests showing on the Lammps list
are related to setting up a system of some sort. Thus, I believe the
input script database has the potential to push Lammps to become the
Gaussian of the classical MD world. But that's just me dreaming here.
Carlos

I agree with you that a different/better interface
is needed. One problem is that Sandia cannot host
a WWW site, like a Wiki, where random people freely post
content. B/c we are a government entity and
then "responsible" for what gets posted, including spam.

So if someone else wants to setup/sponsor such
a site, we'd be very happy to have someone do it.

Steve

I am aware of your site but I think It doesn't appeal to people
because the interface is poor and you guys
didn't try to "milk" the "ultimate currency" that maters to science
people, i.e, citations. Have some ideas but in a nutshell, if you had

been there, done it, doesn't work.

designed a CMS-type site (pretty) where people could link their
scripts to published papers, add comments, etc I think it would have
better chances of taking off. You might have to gather an initial
critical mass of input scripts though. By just looking at the
statistics, the majority of the requests showing on the Lammps list
are related to setting up a system of some sort. Thus, I believe the
input script database has the potential to push Lammps to become the
Gaussian of the classical MD world. But that's just me dreaming here.

the problem is not the hosting. the problem is the culture.
most people that look for help and examples on mailing lists
are at the very beginning of their MD career and are often looking
not for some "good" and "educational" examples, but for something
that does *exactly* what they want to do, without realizing, that
there are no shortcuts in science and that one *has* to learn
certain basics. there ain't no escape from the blues!

so one could make it a little bit easier at the very beginning, but
then the crash is going to be all the harder later on, and matters
only get worse. in any case, at the time when people are the most
capable of providing good help to other newbies, i.e. right after they
figured things out for themselves, most of them are far too intimidated
(better let the "experts" answer that, i cannot afford to expose how
little i know, and it may have misunderstood things and the simulations
in my latest paper could turn be exposed as bogus) or too focused
on producing results with what they just learned, that they will not
want to "waste" time with something that - on the surface - doesn't
provide and personal benefit (only risks). this is ignoring the fact
that one learns *much* more and better by helping others than
through studying yourself. everybody - like you - that makes an
effort to respond and help has to be commended for it and encouraged,
since it *will* pay off. i've been there as well. :wink:

thus in order to get real credit for helping other people in whatever
way, we first need a change in culture that people realize that
a) getting (free!!) help is an obligation to help others later on
b) helping and sharing experiences has to be seen as a way to
    improve the personal skillset *first* and worth the effort.
c) writing tutorials, providing explanations, adding features to a
   software package deserves proper credit just as much as
   providing and maintaining it.

it is rather particular that at a time when sharing the most trivial
things or the most personal details via social networking is quite
normal, the desire to share useful information with colleagues is
at an all time low, at least based on the mailing lists that i am
subscribed to. the lammps mailing list is a pleasant exception.

axel.

Hey Axel,
My comments between your lines.
First of all I appreciate you taking the time to brain storm with
me/us. I'm sure you're way busier
than I am.

I am aware of your site but I think It doesn't appeal to people
because the interface is poor and you guys
didn't try to "milk" the "ultimate currency" that maters to science
people, i.e, citations. Have some ideas but in a nutshell, if you had

been there, done it, doesn't work.

Still, no reason to be discouraged. Content is as powerful as
software. I don't I need to prove
the previous statement to you :wink:

designed a CMS-type site (pretty) where people could link their
scripts to published papers, add comments, etc I think it would have
better chances of taking off. You might have to gather an initial
critical mass of input scripts though. By just looking at the
statistics, the majority of the requests showing on the Lammps list
are related to setting up a system of some sort. Thus, I believe the
input script database has the potential to push Lammps to become the
Gaussian of the classical MD world. But that's just me dreaming here.

the problem is not the hosting. the problem is the culture.
most people that look for help and examples on mailing lists
are at the very beginning of their MD career and are often looking
not for some "good" and "educational" examples, but for something
that does *exactly* what they want to do, without realizing, that
there are no shortcuts in science and that one *has* to learn
certain basics. there ain't no escape from the blues!

Agree on the culture statement. Yet, although most of the posts seem
to come from
newbies I am sure there are more experienced people reading/watching
on the sidelines.
The idea was never to cater to what the newbies might want ('cause in
the majority of
cases they don't even know what they want). The idea is to have
representative scripts of
real life computations, i.e. the PES of alanine dipeptide using the
Amberff03 force field,
a viscosity calculation of liquid hexane using the SLLOD EOM within
NEMD, stuff like that.
Organized in a clever way. Folks that participate in contest like:
http://fluidproperties.org/
have used Lammps for their assignments. I'm sure they wouldn't mind to
contribute their
scripts given that they were meant to be accessible by a jury anyways.
I never suggested the database to be a vehicle for the beginners to
skip any learning
step but for many of us to avoid rediscovering the wheel. I have no
doubt that changing
the culture will be very hard. This is expected as it is just Newton's
first law of motion (inertia)
at play.

so one could make it a little bit easier at the very beginning, but
then the crash is going to be all the harder later on, and matters
only get worse. in any case, at the time when people are the most
capable of providing good help to other newbies, i.e. right after they
figured things out for themselves, most of them are far too intimidated
(better let the "experts" answer that, i cannot afford to expose how
little i know, and it may have misunderstood things and the simulations
in my latest paper could turn be exposed as bogus) or too focused
on producing results with what they just learned, that they will not
want to "waste" time with something that - on the surface - doesn't
provide and personal benefit (only risks).

As to the fear factor... Sure, I can't help it if a researcher likes
to freak out or gets the shivers
when they feel their mistakes might be exposed. But if there is a
"popular" tool that could
give my work better coverage (by sharing my scripts) why wouldn't I
use it? For the less
courageous, linking the scripts to a publication doesn't have to be
mandatory you know?
As to the wasting time, I don't think it would take much time to post
a script with some links
and comments/explanations. We all probably waste much more time
reading our daily emails,
or facebooking somebody, or watching the gangnam style video on youtube :wink:

this is ignoring the fact

that one learns *much* more and better by helping others than
through studying yourself. everybody - like you - that makes an
effort to respond and help has to be commended for it and encouraged,
since it *will* pay off. i've been there as well. :wink:

thus in order to get real credit for helping other people in whatever
way, we first need a change in culture that people realize that
a) getting (free!!) help is an obligation to help others later on
b) helping and sharing experiences has to be seen as a way to
    improve the personal skillset *first* and worth the effort.
c) writing tutorials, providing explanations, adding features to a
   software package deserves proper credit just as much as
   providing and maintaining it.

Agree on the above.

it is rather particular that at a time when sharing the most trivial
things or the most personal details via social networking is quite
normal, the desire to share useful information with colleagues is
at an all time low, at least based on the mailing lists that i am
subscribed to. the lammps mailing list is a pleasant exception.

I believe more than resources (at least at the beginning) it takes
some militants
with little to loose but much to gain to start something like what we
have been discussing
here. Nothing new as it is the same in the entrepreneurial world. And
it will not be
a future academic candidate because they are just too busy trying to
publish papers
in order to build their CVs. In spite of your negative experience
regarding the topic I still
believe that database could be a very powerful add-on to Lammps.

Carlos

Some extra: One could set learning/contest sessions during the Lammps
workshops to teach/ask people how to simulate/compute properties and
later collect those scripts to be posted on the database, etc, etc.
Carlos

I'll forward this to Paul, who plans the workshops.

Steve