Re: [gmx-users] Simulations in vacuo - energy increase
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] Simulations in vacuo - energy increase
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 -- 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] Simulations in vacuo
Zoe Hall skrev 2011-01-11 16.29: Hi gmx-users, I am trying to set up a simulation of a large protein /in vacuo/ using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in vacuum with constant temperature at 300K. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using SHAKE with tolerance 0.001. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used whatsoever. I am not sure, however, what is the appropriate choice for "coulombtype" and other electrostatic parameters for vacuum simulations. I have set "epsilon_r" to 2, as this seems to be an accepted value for proteins but if anyone has comments on this, I would appreciate it. Thanks very much, Zoe Zoe Hall Department of Chemistry Oxford University _zoe.h...@chem.ox.ac.uk_ I should point out that there is probably an error in the methods section. If I recall correctly we used a 0.5 fs timestep. We couldn't get good conservation of total energy with 1 fs steps. Remember to use double precision, or you will again loose conservation of total erergy. Remember to monitor the total energy, because if it's drifting you need to have a more conservative setup, e.g., use a smaller timestep. Take a look at our "follow up" study (Marklund et. al., PCCP (2009) 11 p. 8069--8078) where we used LINCS and managed to conserve the total energy with a 1 fs time step. Good luck! -- --- 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] Simulations in vacuo
On 12/01/2011 2:29 AM, Zoe Hall wrote: Hi gmx-users, I am trying to set up a simulation of a large protein /in vacuo/ using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in vacuum with constant temperature at 300K. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using SHAKE with tolerance 0.001. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used whatsoever. I am not sure, however, what is the appropriate choice for "coulombtype" and other electrostatic parameters for vacuum simulations. I have set "epsilon_r" to 2, as this seems to be an accepted value for proteins but if anyone has comments on this, I would appreciate it. vdwtype = cut-off coulombtype = cut-off and all the distance cut-offs to zero (which is treated as an infinite cut-off) 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
[gmx-users] Simulations in vacuo
Hi gmx-users, I am trying to set up a simulation of a large protein in vacuo using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in vacuum with constant temperature at 300K. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using SHAKE with tolerance 0.001. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used whatsoever. I am not sure, however, what is the appropriate choice for "coulombtype" and other electrostatic parameters for vacuum simulations. I have set "epsilon_r" to 2, as this seems to be an accepted value for proteins but if anyone has comments on this, I would appreciate it. Thanks very much, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- 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
