Dear Jason,
thanks for your detailed answer!
It's interesting to know, that there is a similar undocumented feature
in sander; maybe the next version of the Amber manual will tell us more
about it.
Best regards,
Anselm
Am 04.02.2014 14:45, schrieb Jason Swails:
> On Tue, 2014-02-04 at 14:01 +0100, Anselm Horn wrote:
>> Dear all,
>>
>> in the present version of cpptraj, there exists the possibility to
>> compute a linear interaction energy between two entities in a very
>> convenient way. The lie command then gives vdW and electrostatic
>> contributions.
>>
>> In the AmberTools manuals, however, there is no further literature
>> reference. Does lie use the normal Amber energy function (with the
>> parameter set present in the top file) to compute the vdW energy?
>
> The LIE energy in cpptraj uses the standard potential form for the
> Lennard-Jones, but a rather atypical (for Amber) force- and
> energy-shifted form for the electrostatic interactions (the formula is
> shown in the AmberTools 13 manual for the lie action). No long-range
> correction (either dispersion or electrostatic) is used by cpptraj.
> However, the LIE method reports on differences between the local
> environments of the ligand in a protein and solvent environment so the
> exclusion of long-range effects and shifting of the electrostatic
> potential are unlikely to be detrimental (especially if the cutoff is
> sufficiently large, like 12 A).
>
> Also worth mentioning is the presence of a LIE (called LRT for 'linear
> response theory') calculation option in sander. It is present in Amber
> 12, but not documented in the manual (I believe you can use it by
> specifying "ilrt=1" and "lrtmask" in the &cntrl section of the input
> file -- lrtmask is analogous to the <Ligand Mask> option in cpptraj).
> The sander implementation actually evaluates the energy using the full
> PME electrostatics with a uniform, long-range dispersion correction. (I
> only implemented the LIE action in cpptraj because I was unaware of its
> presence in sander.) I've never used the sander implementation, so I'm
> not sure if ilrt/lrtmask input is all you need, nor do I know in what
> form the output will be (probably in the mdout file in some way).
>
>> What would be the recommended citation for this feature?
>> Just a reference to the AmberTools?
>
> There's a cpptraj citation given at the end of every cpptraj run:
>
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
>
> That is sufficient.
>
> HTH,
> Jason
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 05 2014 - 01:30:04 PST
