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 <jalem...@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 > > 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. > -- 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.