On 2012-08-09 05:56:46AM -0700, Shima Arasteh wrote: > Thanks for replies. > > Some bonds are rotated more than 30 degrees ,as it's written just before > turning off the equilibration. > Is this over-rotation also included in interaction with PBC images?
So the system crashed before LINCS did. Perhaps more energy minimization would be helpful? See what atoms/residues were misbehaving (when LINCS throws those errors, it gives you the atom #) and look at its neighbors to see what sort of large forces might arise. > > Am I supposed to change the rcoulomb and rvdw cutoffs? How would I be sure of > a correct changes? > You are supposed to use the cutoffs appropriate for your forcefield. > > Sincerely, > Shima > > > ----- Original Message ----- > From: Peter C. Lai <p...@uab.edu> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Cc: > Sent: Thursday, August 9, 2012 5:08 PM > Subject: Re: [gmx-users] NVT equilibration > > Parts of your system shifted too much (in Y dimension) for PME to handle. > > What happens to the system up to the point of the crash? > > How large is the system (particle count) vs. # of PME nodes used? > Could be your system is too small for the # of PME nodes used > > Is the protein somehow interacting with its own PBC images? Is there enough > water in the box to shield the protein from seeing itself in the next box > over - it's probably safe to go with a thickness of water around the protein > that is equal to the rcoulomb and rvdw cutoffs (that way you really get 2x > the distance between protein images). > > > On 2012-08-09 05:23:17AM -0700, Shima Arasteh wrote: > > Dear gmx users, > > > > I used the NVT (T=300) equilibration for my system ( a protein in water). > > The first time, I set 100 ps for system for equilibration, It resulted in > > RMSD=3.96 with an average temperature around 299.803 K. > > > > Then I though of a better convergence, so set the equilibration to 200 ps. > > But it stopped due to some error: > > Fatal error: > > 1 particles communicated to PME node 4 are more than 2/3 times the cut-off > > out of the domain decomposition cell of their charge group in dimension y. > > This usually means that your system is not well equilibrated. > > > > > > I'd like to know why such an error might happen? Is a shorter equilibration > > better for NVT generally? > > > > > > Cheers, > > Shima > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
