okk This may be very basic question. I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I picked up one unfolded structure from the trj and solvated with water. I ran em for full system. now i am calculating the entropy. I afraid if i missed something.
I am doing this first time. Pooja > > > On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote: >> I used system (0) for g-covar. >> > > Most likely, g_anaeig is running out of memory. Try using some subset of > the > system, like the protein only or its backbone. > > -Justin > >>> On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: >>>> thanks for reply >>>> >>>> i am using Gromacs 4.5.5 version >>>> command >>>> g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp >>>> >>> >>> What was the g_covar command used to generate the eigenvector .trr >>> file? >>> What >>> group did you choose for analysis during g_covar? >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> ================================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * 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 >>> >> >> >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 * 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
