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 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
