The minimum protein-image distance is less than the value 2.0nm, such as t around 1.6nm above. Does it mean my simulation is failed in the box size set? > 在 2016年8月29日，下午8:58，Justin Lemkul <jalem...@vt.edu> 写道： > > > > On 8/29/16 5:02 AM, YanhuaOuyang wrote: >> Hi, >> I am running a REMD of a disordered protein, I visualized the trajectory >> in VMD and I found that the protein is very close to the box edge. >> Then I use "gmx mindist " to check if a protein has seen its periodic >> image during simulation. When I used the command "gmx mindist -f remd_01.pdb >> -s remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose >> some data from mindist.xvg, they are as follow: >> 0 2.800 5.225 7.200 7.200 7.200 >> 2 2.793 5.136 7.200 7.200 7.200 >> 4 2.804 5.002 7.200 7.200 7.200 >> 6 2.777 5.176 7.200 7.200 7.200 >> 8 2.820 5.187 7.200 7.200 7.200 >> 10 2.871 5.043 7.200 7.200 7.200 >> 12 2.788 5.089 7.200 7.200 7.200 >> 14 2.882 4.892 7.200 7.200 7.200 >> ................ >> 5154 4.153 3.415 7.200 7.200 7.200 >> 5156 4.222 3.483 7.200 7.200 7.200 >> 5158 4.154 3.608 7.200 7.200 7.200 >> 5172 3.607 4.124 7.200 7.200 7.200 >> 5174 3.556 4.140 7.200 7.200 7.200 >> 5176 3.303 4.430 7.200 7.200 7.200 >> 5178 3.291 4.297 7.200 7.200 7.200 >> ................... >> 5880 1.659 5.595 7.200 7.200 7.200 >> 5882 1.787 5.564 7.200 7.200 7.200 >> 5884 1.718 5.575 7.200 7.200 7.200 >> 5886 1.669 5.654 7.200 7.200 7.200 >> 5888 1.636 5.752 7.200 7.200 7.200 >> 5890 1.590 5.761 7.200 7.200 7.200 >> 5892 1.620 5.786 7.200 7.200 7.200 >> 5894 1.513 5.791 7.200 7.200 7.200 >> 5896 1.523 5.908 7.200 7.200 7.200 >> I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance >> between the outside of protein and the edge of box is 1.0 nm. the Minimum >> distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. >> While the deal value should be at least 2.0 nm, which is double the cutoff. >> Do anyone knows the simulation is normal and if a protein has seen its >> periodic image during simulation? > > It has not seen its periodic image with cutoffs = 1.0 nm. You have a very > thin shell of water around the protein, though, which means there could be > some artificial ordering, but whether or not that's enough to seriously > perturb the dynamics is not immediately clear. > >> which group should I choose when i using gmx mindist, protein, C-alpha or >> some else? >> > > Protein. You need to verify that all protein atoms behaved correctly. CA > atoms are unlikely to ever see their own periodic images unless you have done > something horribly wrong in setting up your box. > > -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 <mailto:jalem...@outerbanks.umaryland.edu> > | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > <http://mackerell.umaryland.edu/~jalemkul> > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send > a mail to gmx-users-requ...@gromacs.org > <mailto: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.
