Re: [gmx-users] Re: force autocorrelation

that I need the force autocorrelation for the forces >> acting on a single atom. Will the method >> >> 1. Run mdrun with nstfout set appropriately >> 2. g_traj -h >> 3. g_analyze -h >> >> >> work here >> >> Keith >> >> >>

[gmx-users] pdb2gmx Could not find force field, when using -ff commandline parameter

ing the GMXDATA path (it was blank) to the path that contains ffG45a3.itp in /usr/share. No luck there either. Anyone have any ideas? Thanks, Keith -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.grom

[gmx-users] Can't build gromacs-4.5.3 with cmake

pty in CMakeLists.txt is ${LIB_INSTALL_DIR}. Does anyone know what that might be caused by? Thank you, Keith Callenberg -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Sear

[gmx-users] Can't build gromacs-4.5.3 with cmake

I am running cmake version 2.8.0 on Ubuntu 10.04 64-bit with gcc 4.4.3. ~/apps/gromacs-4.5.3$ cmake -version cmake version 2.8.0 Thanks, Keith >What cmake version are you using? > >On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg wrote: >> Hello gmx-users, >> >> I

Re: [gmx-users] Can't build gromacs-4.5.3 with cmake

run into this issue as well. The (inelegant) workaround was to compile as sudo: sudo make mdrun (and) sudo make install-mdrun. Now it works. Thank you! Keith -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

Re: [gmx-users] Simulations on GPU

ovided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith > > Rossen > -- > gm

Re: [gmx-users] Simulations on GPU

) (G96Angle). >> >> Maybe it's possible to run a short simulation on a small system and >> not encounter the missing interactions? I don't know enough about how >> the forcefields work to know whether that would get past the error. >> >> -Keith >>

[gmx-users] Understanding the output of g_rmsf

the reference frame/structure?   Many thanks,    Keith Keith D. Ball, PhD Staff Scientist Catalyst Biosciences 290 Utah Ave S. San Francisco, CA 94080 650-266-8661 (phone) 650-871-2475 (fax) [EMAIL PROTECTED] http://www.catbio.com

[gmx-users] Group-specific differences in RMS fluctuation results via g_rmsf

osition of its atoms, and not dependent upon some external "frame". Should I just use the whole protein as the reference, and extract the residue values of interest by hand? Thanks, Keith Keith D. Ball, PhD Staff Scientist Catalyst Biosciences 290