[gmx-users] question on ffG43a1p force field

[Justin Lemkul]

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

-- 
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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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