Re: [gmx-users] Re: Simluations in vacuum - energy increase
On 2/05/2011 4:00 AM, Zoe Hall wrote: Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says "hbonds", not "h-bonds", however didn't make much difference which one I used. "h-bonds" is correct. The manual's been wrong for nearly a decade(!). I've fixed it. Mark -- 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
Re: [gmx-users] Re: Simluations in vacuum - energy increase
David van der Spoel skrev 2011-05-01 20.10: On 2011-05-01 20.00, Zoe Hall wrote: Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says "hbonds", not "h-bonds", however didn't make much difference which one I used. Could someone suggest the reason why you would want to turn temperature coupling off during the simulations - I don't really understand this. In our work we want to study evaporation and cooling induced by the leaving water molecules. If you don't have water molecules, or even assume some kind of heat bath (e.g. a gas atmosphere), you could turn on T-coupling. We furthermore managed to simulate lysozyme in vacuo with 1 fs time steps, without energy drift. See Marklund et. al. PCCP v. 11:36, pp. 7741 (2009) for clues. Thanks, Zoe On 2011-04-30 14.17, Zoe Hall wrote: Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method. integrator = md tinit = 0 dt = 0.001 nsteps = 1000 nstxout = 2 nstvout = 2 nstfout = 0 nstlog = 10 nstenergy = 10 nstxtcout = 2 energygrps = Protein nstcomm = 5 nstlist = 0 ns-type = simple pbc = no rlist = 0 coulombtype = Cut-off rcoulomb = 0 epsilon_r = 2 vdw-type = Cut-off rvdw =0 Tcoupl = no tc-grps = Protein tau_t = 0.1 ref_t = 300 Pcoupl = no Pcoupltype = Isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University _zoe.h...@chem.ox.ac.uk_ Are you sure h-bonds are being constrained, because otherwise the time step is too large? (maybe you need to write h-bonds). You may need to increase the constraint accuracy as well. We did all our vacuum calcs in double precision as well IIRC. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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
Re: [gmx-users] Re: Simluations in vacuum - energy increase
On 2011-05-01 20.00, Zoe Hall wrote: Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says "hbonds", not "h-bonds", however didn't make much difference which one I used. Could someone suggest the reason why you would want to turn temperature coupling off during the simulations - I don't really understand this. In our work we want to study evaporation and cooling induced by the leaving water molecules. If you don't have water molecules, or even assume some kind of heat bath (e.g. a gas atmosphere), you could turn on T-coupling. Thanks, Zoe On 2011-04-30 14.17, Zoe Hall wrote: Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method. integrator = md tinit = 0 dt = 0.001 nsteps = 1000 nstxout = 2 nstvout = 2 nstfout = 0 nstlog = 10 nstenergy = 10 nstxtcout = 2 energygrps = Protein nstcomm = 5 nstlist = 0 ns-type = simple pbc = no rlist = 0 coulombtype = Cut-off rcoulomb = 0 epsilon_r = 2 vdw-type = Cut-off rvdw =0 Tcoupl = no tc-grps = Protein tau_t = 0.1 ref_t = 300 Pcoupl = no Pcoupltype = Isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University _zoe.h...@chem.ox.ac.uk_ Are you sure h-bonds are being constrained, because otherwise the time step is too large? (maybe you need to write h-bonds). You may need to increase the constraint accuracy as well. We did all our vacuum calcs in double precision as well IIRC. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Re: Simluations in vacuum - energy increase
Hi - thanks - much improved with shorter timestep and increase in constraint accuracy. Manual says "hbonds", not "h-bonds", however didn't make much difference which one I used. Could someone suggest the reason why you would want to turn temperature coupling off during the simulations - I don't really understand this. Thanks, Zoe On 2011-04-30 14.17, Zoe Hall wrote: > Gmx-users, > > I am trying to carry out a simulation of lysozyme in vacuo using the > OPLS-AA forcefield. After energy minimisation, the protein is run for > 10ps with position restraints and temperature coupling on. This is > followed by the full production run of 10ns with temperature and > pressure coupling turned off, H bonds are constrained using LINCS and a > time step of 1fs. For vacuum conditions, the periodic boundary > conditions are turned off, and no cut-offs are used. When I carry out > the 10ns simulation the total energy gradually increases, as does the > temperature from 300 to 500K. I presume this is because the temperature > coupling is turned off, however that is what I have noted from the > literature that others do for their vacuum simulations. Can anyone shed > any light on this? Following is my method. > > integrator = md > > tinit = 0 > > dt = 0.001 > > nsteps = 1000 > > nstxout = 2 > > nstvout = 2 > > nstfout = 0 > > nstlog = 10 > > nstenergy = 10 > > nstxtcout = 2 > > energygrps = Protein > > nstcomm = 5 > > nstlist = 0 > > ns-type = simple > > pbc = no > > rlist = 0 > > coulombtype = Cut-off > > rcoulomb = 0 > > epsilon_r = 2 > > vdw-type = Cut-off > > rvdw =0 > > Tcoupl = no > > tc-grps = Protein > > tau_t = 0.1 > > ref_t = 300 > > Pcoupl = no > > Pcoupltype = Isotropic > > tau_p = 1 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > gen_vel = yes ; > > gen_temp = 300.0 > > gen_seed = -1 > > constraints = hbonds > > constraint-algorithm = LINCS > > lincs_order = 4 > > Thanks, > > Zoe > > Zoe Hall > > Department of Chemistry > > Oxford University > > _zoe.h...@chem.ox.ac.uk_ > Are you sure h-bonds are being constrained, because otherwise the time step is too large? (maybe you need to write h-bonds). You may need to increase the constraint accuracy as well. We did all our vacuum calcs in double precision as well IIRC. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
