Hi,
On Wed, Jun 29, 2022 at 6:31 AM <gsormani.ictp.it> wrote:
>
> Hi Daniel,
> I imagine then that Amber20 is a previous version than 5.3.7.
Yes, amber20 ships with 5.1.0 I think.
> What is strange is that I use Amber16 on a different server and there
> loading the topology (always with 12-6-4 LJ parameters) on cpptraj I don't
> have any warning. Are previous versions of cpptraj simply ignoring the c4
> term without telling?
Effectively yes. I don't remember when the Lennard Jones C
coefficients were introduced, but I think at that point (amber 16)
cpptraj was skipping unrecognized FLAGs silently unless a debug level
had been set.
> Can I be sure that the simulation is actually using the 12-6-4 LJ
> potential once the flag "lj1264 = 1" is in the output of the pmemd.cuda ?
I think that if that flag is set the simulation will use the 12-6-4
potential, but I haven't ever used it myself so I'm not sure what
error checking is in place.
>
> Could you please give me some extra details about the possibility of using
> esander to print the c4/r4 term?
You would pass the 'lj1264 1' keyword to the esander command, but
since I don't think even sander can specifically split out the r4
component of the 12-6-4 potential, this probably won't help you. You
may need to dive into the sander code directly to have it print what
you want. Others with more 12-6-4 experience may want to chime in
here.
>
> Sorry if my questions are basic, I started to use Amber very recently.
Don't apologize for asking questions - that's what the list is here for!
-Dan
>
> Many thanks!
> Giulia
>
> > Hi,
> >
> > Support for reading/writing LENNARD_JONES_CCOEF read/write was added
> > in version 5.3.7. However, none of the native energy functions in
> > cpptraj support calculating the 12-6-4 potential yet. You may be able
> > to get it to work with 'esander' (if cpptraj was compiled with
> > libsander support) but this is untested.
> >
> > -Dan
> >
> > On Wed, Jun 29, 2022 at 5:00 AM Giulia Sormani via AMBER
> > <amber.ambermd.org> wrote:
> >>
> >> Good morning to everyone,
> >>
> >> To simulate the binding of an organic molecule to Zr4+ ion I am using
> >> the
> >> 12-6-4 LJ potential (on Amber20).
> >> I think that the c4 parameter is actually taken into account during the
> >> simulation, indeed in the section Potential Function of the output file
> >> of
> >> pmemd.cuda there is the flag "lj1264 = 1".
> >> However, when I load the topology file in cpptraj I get the following
> >> mistake:
> >> "Warning: Amber topology flag 'LENNARD_JONES_CCOEF' is unrecognized and
> >> will be skipped" .
> >>
> >> Can someone help me with this?
> >>
> >> I also have another question: is there a way to print the c4/r^4 energy
> >> component between two atoms along the simulation?
> >> I tried to search an action of cpptraj doing so, the pairwise action
> >> evaluates the vdw energy between group of atoms, but not the single
> >> components.
> >>
> >> best,
> >>
> >> Giulia
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Thu Aug 04 2022 - 13:33:51 PDT
