[gmx-users] gmx mdmat calculation of heavy atoms of two side chains

Dear gmx users, I would like to know about the hydrophobic interaction between heavy atoms of side chains in different chains of peptides. How can I use mdmat tool for this calculation? I separately indexed all heavy atoms but mdmat use only one index group in the calculation. I re-integrated

Re: [gmx-users] Question on force field

Dear Justin, Thank you very much. I get it now.Best regards,Ouyang At 2017-07-31 10:46:10, "Justin Lemkul" wrote: > > >On 7/30/17 8:58 PM, YanhuaOuyang wrote: >> Hi, >> I have run a protein MD simulation and choose a force field "8: CHARMM27 >> all-atom force field (CHARM22

Re: [gmx-users] Question on force field

On 7/30/17 8:58 PM, YanhuaOuyang wrote: Hi, I have run a protein MD simulation and choose a force field "8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder that whether the CHARMM27 all-atom force field here is equal to the CHARMM22/CMAP Well, not "equal" but

[gmx-users] Question on force field

Hi, I have run a protein MD simulation and choose a force field "8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder that whether the CHARMM27 all-atom force field here is equal to the CHARMM22/CMAP -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] problem on Gromacs 4.5.7 installation

Hi, On Sun, 30 Jul 2017 20:35 Rahma Dahmani wrote: > Dear gmx-users, > I am trying to install Gromacs 4.5.7 There's essentially no reason to install a version that has been unsupported for over three years. Do yourself a favour and use a code version that has had

[gmx-users] problem on Gromacs 4.5.7 installation

Dear gmx-users, I am trying to install Gromacs 4.5.7 and i choose to run it with cmake 3.9.0 and fftw 3.3.6 i succeeded to install cmake files but i have a problem with fftw installtion: its a 'make install' problem: make[3]: *** [install-includeHEADERS] Erreur 1 make[3]: quittant le répertoire «

Re: [gmx-users] compiling ambconv

Hi, That isn't a GROMACS tool, so after trying a websearch, please ask in a more suitable forum. Mark On Sun, 30 Jul 2017 16:23 Vidya R wrote: > Hi gromacs users, > > How to compile ambconv extracted from ambconv.tgz? > > > Thanks, > Vidya R > -- > Gromacs Users

[gmx-users] compiling ambconv

Hi gromacs users, How to compile ambconv extracted from ambconv.tgz? Thanks, Vidya R -- 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 *