VMD-L Mailing List

From: Rasoul Nasiri (nasiri1355_at_gmail.com)
Date: Tue Dec 24 2013 - 11:42:25 CST

first off, please always copy the mailing list on your reply and don't
reply just to individual people.

On Tue, Dec 24, 2013 at 12:33 PM, Rasoul Nasiri <nasiri1355_at_gmail.com>
wrote:
> Thanks Alex for your reply.
>
> In this case, I think gromacs tools would not be suitable for analysis of
my
> trajectories obtained by ReaxFF. Is'n it?

how should *I* know? i didn't do your simulation, i don't know what
data you collected and i don't know what information you want to
extract from your simulation.

> Which tools do you suggest for dynamic analysis of my system?

your question is backwards. in fact, your entire procedure seems
backwards. if you don't know what kind of analysis you need and with
which tools you want to perform it, how can you even plan and design a
simulation? particularly with reaxff, you need to make sure that you
write out suitable information, e.g. about charges and bond orders, so
you can later post process it. of course, because of the special
nature of reaxff, you have to deal with similar issue than, say, with
semi-empirical or ab initio calculations, where part of the
postprocessing is very model specific and requires writing out or
post-processing intermediate data.

Sorry, I was assuming that analyses are under consideration which can be
influenced by charges and chemical bonds since those are being collected in
*.tpr.

If charges and bonds are considered as fixed values in .tpr, how one can
perform the
analysis properly? Having said this, is there any way one considers
flexible values for
those in .tpr file?

For an example, I'm interest to know how much chemical bonds affect dynamic
behavior
of molecules in interface (liquid-gas) and finally on heat and mass
transfers on fuel droplets in
nano-scale.

Best,
Rasoul

On Tue, Dec 24, 2013 at 12:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> first off, please always copy the mailing list on your reply and don't
> reply just to individual people.
>
> On Tue, Dec 24, 2013 at 12:33 PM, Rasoul Nasiri <nasiri1355_at_gmail.com>
> wrote:
> > Thanks Alex for your reply.
> >
> > In this case, I think gromacs tools would not be suitable for analysis
> of my
> > trajectories obtained by ReaxFF. Is'n it?
>
> how should *I* know? i didn't do your simulation, i don't know what
> data you collected and i don't know what information you want to
> extract from your simulation.
>
> > Which tools do you suggest for dynamic analysis of my system?
>
> your question is backwards. in fact, your entire procedure seems
> backwards. if you don't know what kind of analysis you need and with
> which tools you want to perform it, how can you even plan and design a
> simulation? particularly with reaxff, you need to make sure that you
> write out suitable information, e.g. about charges and bond orders, so
> you can later post process it. of course, because of the special
> nature of reaxff, you have to deal with similar issue than, say, with
> semi-empirical or ab initio calculations, where part of the
> postprocessing is very model specific and requires writing out or
> post-processing intermediate data.
>
> axel.
>
> > Please note that I'm dealing with highly extreme conditions (combustion)
> in
> > which bonds and charges should be updated.
> >
> > Best,
> > Rasoul
> >
> >
> > On Tue, Dec 24, 2013 at 11:29 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Tue, Dec 24, 2013 at 9:30 AM, Rasoul Nasiri <nasiri1355_at_gmail.com>
> >> wrote:
> >> > Dear all,
> >> >
> >> > I have been trying to build up a tpr file in order to analysis my MD
> >> > simulations by GROMACS.
> >> >
> >> > 1- My potential (ReaxFF) is not supported GROMCAS, therefore I have to
> >> > construct tpr file manually, hopefully by VMD.
> >>
> >> the topotools supports writing out a "fake" .top file that would allow
> >> building a similarly fake .tpr file sufficient for most analysis tasks
> >> in gromacs.
> >>
> >> > 2- All bonds/charges are updated based on the bond order method.
> >>
> >> > I just wondering whether there is any plug in in VMD can consider
> point
> >> > of
> >> > (2) for constructing a .tpr?
> >>
> >> that would be utterly pointless, since the very basic assumption of a
> >> .tpr file is that bonds and charges don't change (like VMD does, too).
> >> with bond orders you don't really have a simple "is this is a bond?
> >> yes/no" decision anyway. but rather you have a dynamic range.
> >>
> >> axel.
> >>
> >> > Best,
> >> > Rasoul
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>