Hi again,
I know of now formula that allows you to directly convert the input flags
from Amber to Gromacs. For our work we did this by hand, with an initial
guess on the Gromacs flags and then slight refinement of them through trial
and error. The refinement is done by comparing observables between
calculations done by both programs. For example, one can use the molecular
mechanics energies from single-point calculations, or even better from full
optimizations to compare the results between the two programs. For MD
simulations you can use other dynamic-dependent observables. I hope this
helps some.
Bests,
Karl
On Mon, May 6, 2019 at 1:12 PM Akshay Prabhakant <akshayresearch16.gmail.com>
wrote:
> Thank you for your help, Mr.Kirschner. I was actually inquiring about a
> method wherein, for a given mdin input file in amber-md, what will be the
> corresponding ".mdp" file in gromacs, keeping in mind that I want to use
> amber-forcefield in both the softwares.
>
> On Mon, May 6, 2019 at 4:03 PM Karl Kirschner <k.n.kirschner.gmail.com>
> wrote:
>
> > Hello Akshay,
> >
> > There is a very nice tool called ACPYPE, written by Alan W Sousa da
> Silva
> > and Wim F Vranken [1]. You can download it at
> > https://github.com/alanwilter/acpype . We have recently ensured that 1-4
> > scaling is correctly done within this tool, meaning that Glycam06 is now
> > converted correctly [2] in addition to the other Amber force fields. We
> did
> > an extensive study to ensure that the parameters generate molecular
> > mechanics and MD observables that are essentially the same (i.e. within a
> > very small error) for a given Amber leap topology file is used in Amber
> and
> > when converted and used in Gromacs.
> >
> > 1. SOUSA DA SILVA, A. W. & VRANKEN, W. F. ACPYPE - AnteChamber PYthon
> > Parser interfacE. BMC Research Notes 2012, 5:367
> > doi:10.1186/1756-0500-5-367 http://www.biomedcentral.com/1756-0500/5/367
> >
> > 2. Austen Bernardi, Roland Faller, Dirk Reith and Karl N. Kirschner,
> ACPYPE
> > update for Nonuniform 1--4 Scale Factors: Conversion of the GLYCAM06
> Force
> > Field from AMBER to GROMACS, SoftwareX, accepted on April 25, 2019.
> >
> > Bests,
> > Karl
> >
> > On Mon, May 6, 2019 at 11:59 AM Akshay Prabhakant <
> > akshayresearch16.gmail.com> wrote:
> >
> > > Just like this page <http://ambermd.org/namd/namd_amber.html>, which
> > shows
> > > conversion of amber-md input-parameter values into equivalent values
> for
> > > namd-input file, can anyone suggest me a way of converting amber-md
> > > input-parameters to gromacs-md input-paramters(using amber forcefield)?
> > > Thanks in advance.
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Received on Tue May 07 2019 - 00:30:01 PDT
