Dear Justin, Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints? If the difference is quite small, then I can choose constraining bonds to increase time step.
Thanks a lot. -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 18 May 2015 9:44 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/18/15 7:39 AM, Ming Tang wrote: > Dear Justin, > > After minimization, I got the following note when using NPT. > > NOTE 1 [file topol.top, line 49]: > The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has > an estimated oscillational period of 1.0e-02 ps, which is less than 10 > times the time step of 1.0e-03 ps. Maybe you forgot to change the > constraints mdp option. > > Does this has something to do with the warning given by pdb2gmx? > When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there > anything wrong with my topol.top? > No, as the note says, you probably aren't using constraints, which if you want a 1-fs or larger value of dt, you need to be using. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
