[gmx-users] restraining ligand for position restraint simulation

1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 HSL 1 SOL 1 SOL 12480 Na 11 So

[gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps

rest of the time steps (up to 20ps) were roughly around 1150. I'm wondering why the energy at the start is so low for my protein (which I energy minimized)...I assumed it would be near 1150. Is this a problem/what does it mean? Os it fine to move on and do an mdrun? Thanks so much, Halie

[gmx-users] np command with GROMACS 4.0.4

? Thanks so much! Halie Shah University of Houston, TX U.S. Briggs Lab ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

[gmx-users] trajectory file not moving in vmd

Thanks in advance, Halie Shah University of Houston Computational Biology Lab ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!

[gmx-users] solvent box outside protein

? Thanks much in advance, Halie Shah ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests t

[gmx-users] grompp command: The solvent group SOL is not continuous

nts Select a group: 13 Selected 13: 'SOL' --- Program genion, VERSION 4.0.4 Source code file: ../../../src/tools/gmx_genion.c, line: 434 Fatal error: The solvent group SOL is not continuous: index[3]=2403, index[4]=2417 -----