[gmx-users] question on ffG43a1p force field

[Lei Qian]

Thank you Dr. Lemkul,
I continued to use the GROMOS 43a1p for my simulation.

I did simulation for 2 proteins separately: one is WT, the other one is its
one-residue mutant.
And I finished em, NVT, NPT and 1 ns Production (4 steps) for both proteins.

However, I found for each of these 4 above steps, the wall time was a lot
more longer for mutant than WT protein.
Actually I used the same set of parameters for both proteins: e.g. same mdp
files for both protein in each step.
Both proteins get acceptable results after 100-step NVT, 100-step NPT etc.,
but the wall-time for mutant was much more longer than WT.
Could I ask the reason for this?
Sorry for this inconvenience. Thank you for your time and all your help!
Lei








On Tue, Aug 20, 2019 at 8:23 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/20/19 2:11 AM, Lei Qian wrote:
> > Thank you Dr. Lemkul,
> > Could I ask one more question? Thank you!
> >
> > When I did the step for adding ions and minimization and equilibration
> > steps, one warning always showed up.
> > So I had to add -maxwarn 2 after the command gmx grompp.
> > This warning is as follows:
> >
> > WARNING 1 [file topol.top, line 48]:
> >    The GROMOS force fields have been parametrized with a physically
> >    incorrect multiple-time-stepping scheme for a twin-range cut-off. When
> >    used with a single-range cut-off (or a correct Trotter
> >    multiple-time-stepping scheme), physical properties, such as the
> density,
> >    might differ from the intended values. Check if molecules in your
> system
> >    are affected by such issues before proceeding. Further information
> may be
> >    available at https://redmine.gromacs.org/issues/2884.
> >
> > It seems this warning is related to the GROMOS force field (for
> > phosphorylation) you sent to me last week.
> > Could I disregard this warning?
>
> There are significant concerns about the reproducibility of GROMOS force
> fields. The authors of a recent study (
> https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) allege that GROMACS
> has bugs that affect results, but the GROMACS developers maintain that
> the GROMOS force fields were developed with incorrect algorithms in the
> GROMOS software (hence the warning, and see the related Redmine issue
> linked in the message).
>
> The issue is not specifically related to 43a1p (which is anyway an
> extremely old force field), but all of the GROMOS parameter sets.
>
> Proceed with caution. There are other force field options available that
> have been confirmed to work as expected across different software.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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