[gmx-users] minimization is not converging
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Thu Sep 6 16:25:26 CEST 2018
Thank you sir
On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> On 9/6/18 10:09 AM, Bratin Kumar Das wrote:
> > Respected Dr. Justin
> > To avoid the complicacy I solvated
> > only the protein pdb in a pbc box and tried for minimizatin. There also
> > minimization is not converging. Sir, till now I learned to carry out
> > protein ligand system md simulation successfully. I tried all possible
> > to simulate the my membrane protein system. I failed. Is it possible that
> > the PDB file itself have some serious issue with its coordinates. the
> > structure refinement is required may be.
> It may, and I have already suggested a few things for you to check.
> Please do so.
> If you can provide more specific diagnostics of what is happening,
> someone on this list might be able to suggest something. What you've
> provided thus far is a generic instability that no one can diagnose.
> Investigate the structure, check for pdb2gmx warnings, follow the
> diagnostics I've already suggested, and report back with specific
> observations, a PDB code, and exact errors or warnings you get from any
> program if you need further help.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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-request at gromacs.org.
More information about the gromacs.org_gmx-users