[gmx-users] Compiling GROMACS w CUDA 5.0 problem

2013-05-26 Thread Jernej Zidar
Hi, I want to compile GROMACS to support CUDA. First I do a cmake: CMAKE_PREFIX_PATH=/scratch/ihpc/ihpczidj/local/bin/:/usr/local/CUDA/5.0/ cmake ../gromacs-4.6 -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/scratch/ihpc/ihpczidj/

[gmx-users] AMBER99 P450 heme topology

2013-05-26 Thread Parker de Waal
Hi Everyone, I've been looking running MD simulations on heme containing P450s using the AMBER99 force field however have bee having a hard time generating or finding a usable topology file for the heme cofactor. Does anyone have any recommendations for heme topology files and how to use them? T

Re: [gmx-users] mdrun outputs incorrect resnames

2013-05-26 Thread Reid Van Lehn
Great, thank you that did the trick. My fault for not realizing this earlier. Best, Reid On Sun, May 26, 2013 at 2:12 AM, Tsjerk Wassenaar wrote: > No, the residue names are the those from the .top file. But that's not the > same as the moleculetypes. You have to change the residue names in th

[gmx-users] Re: g_hbond

2013-05-26 Thread maggin
Hi, Erik Thank you very much!Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008548.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/

[gmx-users] Entropy

2013-05-26 Thread Yulian
Dear Gromacs users, There is a problem with entropy calculations with g_anaeig. I have 3 runs 100 ns each. Entropy for each run (Protein-H) is round 31000 J/mol K (100 ns) If I use trjcat to connect two trajectories it is 26000 J/mol K (200 ns) For three connect trajectories it is round 19000 J/