[gmx-users] Explicit silvent together with implicit solvent model
Dear Gromacs developer: · I would like to simulate a reaction with 50 explicit water molecules with QM/MM (orca/gmx), and then add a implicit solvent model around this cluster (reaction center + 50 waters). But when I search the gromacs mailing list and gromacs manual, I get this “With the release of GROMACS version 4.5, it is possible to conduct simulations using implicit solvent models;…….” I was wondering is there any possibility to perform QM/MM calculation (orca/gmx) along with implicit solvent model? Thanks in advance. -- 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/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] Explicit solvent together with implicit solvent
Dear gromacs developers: I would like to simulate a reaction with 50 explicit water molecules with QM/MM (orca/gmx), and then add a implicit solvent model around this cluster (reaction center + 50 waters). But when I search the gromacs mailing list and gromacs manual, I get this “With the release of GROMACS version 4.5, it is possible to conduct simulations using implicit solvent models;…….” I was wondering is there any possibility to perform QM/MM calculation (orca/gmx) along with implicit solvent model? Thanks in advance. Yan Li -- 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/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] Explicit solvent together with implicit solvent
Dear gromacs developers: I would like to simulate a reaction with 50 explicit water molecules with QM/MM (orca/gmx), and then add a implicit solvent model around this cluster (reaction center + 50 waters). But when I search the gromacs mailing list and gromacs manual, I get this “With the release of GROMACS version 4.5, it is possible to conduct simulations using implicit solvent models;…….” I was wondering is there any possibility to perform QM/MM (orca/gmx) along with implicit solvent model? Thanks in advance. Yan -- 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/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] gromacs/orca--qmmm
Dear Gromacs developers: I'm trying to run a QM-MM single point energy calculation on a structure (a small molecule with 50 water molecules with no pbc, no cutoff). I use orca for QM part amd gromacs for MM part. But when I run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly and terminate naormally, but after that mdrun run stops with a segmentation fault. Here is the error information: *Back Off! I just backed up sp.log to ./#sp.log.1#**Reading file sp.tpr, VERSION 4.5.5 (single precision)**QM/MM calculation requested.**there we go!**Layer 0**nr of QM atoms 9**QMlevel: MP2/3-21G* */home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360...**orca initialised...* *Back Off! I just backed up traj.trr to ./#traj.trr.1#* *Back Off! I just backed up ener.edr to ./#ener.edr.1#**starting mdrun 'Protein'**0 steps, 0.0 ps.**Calling '/home/li/programs/orca_x86_64_exe_r2360/orca /home/li/Test/test_gmx/qmmm/test/sp.inp >> /home/li/Test/test_gmx/qmmm/test/sp.out'**Segmentation fault* Here is my sp.mdp title= test cpp =/lib/cpp integrator = md nsteps = 0 dt = 0.001 ;constraints = none emtol= 10.0 emstep = 0.01 nstcomm = 1 ns-type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 tcoupl = no pcoupl = no gen-vel = no nstxout = 1 nstlog = 1 nstenergy= 1 nstvout = 1 nstfout = 1 pbc = no comm_mode= angular ; non-equilibrium md freezegrps = System freezedim= y y y xtc_grps = System energygrps = System ;qmmm calculation QMMM = yes QMMM-grps= QMatoms QMMMscheme = normal QMmethod = MP2 QMbasis = 3-21g QMcharge = 0 QMmult = 1 The *.ORCAINFO is: *! RKS b3lyp/g sv(p) tightscf* And I also tried QMMMsheme=ONIOM, but I get the segmentation fault too. Am I missing something in all of this? Any help would be highly appreciated. -- 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/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] qm/mm(orca/gromacs)
Dear Gromacs developers: I'm trying to run a QM-MM single point energy calculation on a structure (a small molecule with 50 water molecules with no pbc, no cutoff). I use orca for QM part amd gromacs for MM part. But when I run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly and terminate naormally, but after that mdrun run stops with a segmentation fault. Here is the error information: Back Off! I just backed up sp.log to ./#sp.log.1# Reading file sp.tpr, VERSION 4.5.5 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 9 QMlevel: MP2/3-21G /home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360... orca initialised... Back Off! I just backed up traj.trr to ./#traj.trr.1# Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein' 0 steps, 0.0 ps. Calling '/home/li/programs/orca_x86_64_exe_r2360/orca /home/li/Test/test_gmx/qmmm/test/sp.inp >> /home/li/Test/test_gmx/qmmm/test/sp.out' Segmentation fault Here is my sp.mdp title= test cpp =/lib/cpp integrator = md nsteps = 0 dt = 0.001 ;constraints = none emtol= 10.0 emstep = 0.01 nstcomm = 1 ns-type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 tcoupl = no pcoupl = no gen-vel = no nstxout = 1 nstlog = 1 nstenergy= 1 nstvout = 1 nstfout = 1 pbc = no comm_mode= angular ; non-equilibrium md freezegrps = System freezedim= y y y xtc_grps = System energygrps = System ;qmmm calculation QMMM = yes QMMM-grps= QMatoms QMMMscheme = normal QMmethod = MP2 QMbasis = 3-21g QMcharge = 0 QMmult = 1 The *.ORCAINFO is: ! RKS b3lyp/g sv(p) tightscf And I also tried QMMMsheme=ONIOM, but I get the segmentation fault too. Am I missing something in all of this? or the orca/gromcas can not be used to non periodic system? Any help would be highly appreciated. Thanks Yan -- 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/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
