Re: [gmx-users] Re: Protein in vacum
YES. On Mon, Jan 28, 2013 at 12:51 PM, Shima Arasteh wrote: > > > Am I supposed to skip this step? > > > Thanks for your reply. > > Sincerely, > Shima > ___ > From: Dr. Vitaly Chaban > To: gmx-us...@gromuracs.org > Sent: Monday, January 28, 2013 3:17 PM > Subject: [gmx-users] Re: Protein in vacum > >> >> Dear users, >> >> I have done simulation with my protein in water earlier successfully using >> CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the >> last simulation of protein-water. When I go to the NPT equilibration, I get >> a fatal error. >> The commands I ran: >> >> The npt.mdp file settings are: >> ; Parameters describing neighbors searching and details about interaction >> calculations >> ns_type= grid; Neighbor list search method (simple, grid) >> nstlist= 5; Neighbor list update frequency (after every >> given number of steps) >> rlist= 1.2; Neighbor list search cut-off distance (nm) >> rlistlong = 1.4 >> rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) >> rvdw= 1.2 ; short-range van der Waals cutoff (in nm) >> vdwtype = switch >> rvdw_switch = 0.8 >> ; Parameters for treating bonded interactions >> continuation= no; Whether a fresh start or a continuation from a >> previous run (yes/no) >> constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) >> constraints= all-bonds; Which bonds/angles to constrain (all-bonds / >> hbonds / none / all-angles / h-angles) >> lincs_iter= 1; Number of iterations to correct for rotational >> lengthening in LINCS (related to accuracy) >> lincs_order= 4; Highest order in the expansion of the constraint >> coupling matrix (related to accuracy) >> >> ; Parameters for treating electrostatic interactions >> coulombtype= PME; Long range electrostatic interactions >> treatment (cut-off, Ewald, PME) >> pme_order= 4; Interpolation order for PME (cubic interpolation >> is represented by 4) >> fourierspacing= 0.16; Maximum grid spacing for FFT grid using >> PME (nm) >> >> ; Temperature coupling parameters >> tcoupl= Nose-Hoover; Modified Berendsen thermostat using >> velocity rescaling >> tc-grps= Protein ; Define groups to be coupled separately to >> temperature bath >> tau_t= 0.5; Group-wise coupling time constant (ps) >> ref_t= 310 ; Group-wise reference temperature (K) >> >> ; Pressure coupling parameters >> pcoupl= Parrinello-Rahman; Pressure coupler used under NPT >> conditions >> pcoupltype= isotropic; Isotropic scaling in the x-y >> direction, independent of the z direction >> tau_p= 5.0; Coupling time constant (ps) >> ref_p= 1.0; Reference pressure for coupling, x-y, z >> directions (bar) >> compressibility = 4.5e-54.5e-5; Isothermal compressibility >> (bar^-1) >> refcoord_scaling = com > > > > Vacuum is incompatible with pressure coupling. > > > Dr. Vitaly V. Chaban > MEMPHYS - Center for Biomembrane Physics > Department of Physics, Chemistry and Pharmacy > University of Southern Denmark > Campusvej 55, 5230 Odense M, Denmark > -- > 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 -- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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: Protein in vacum
On 1/28/13 6:51 AM, Shima Arasteh wrote: Am I supposed to skip this step? Do not be tempted to think that there is a "standard" or "required" workflow. The ensembles and environments you choose are dependent upon the task at hand. There may be common workflows for proteins in water, but even those are not set in stone. -Justin Thanks for your reply. Sincerely, Shima ___ From: Dr. Vitaly Chaban To: gmx-us...@gromuracs.org Sent: Monday, January 28, 2013 3:17 PM Subject: [gmx-users] Re: Protein in vacum Dear users, I have done simulation with my protein in water earlier successfully using CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the last simulation of protein-water. When I go to the NPT equilibration, I get a fatal error. The commands I ran: The npt.mdp file settings are: ; Parameters describing neighbors searching and details about interaction calculations ns_type= grid; Neighbor list search method (simple, grid) nstlist= 5; Neighbor list update frequency (after every given number of steps) rlist= 1.2; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints= all-bonds; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter= 1; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order= 4; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype= PME; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order= 4; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing= 0.16; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl= Nose-Hoover; Modified Berendsen thermostat using velocity rescaling tc-grps= Protein ; Define groups to be coupled separately to temperature bath tau_t= 0.5; Group-wise coupling time constant (ps) ref_t= 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl= Parrinello-Rahman; Pressure coupler used under NPT conditions pcoupltype= isotropic; Isotropic scaling in the x-y direction, independent of the z direction tau_p= 5.0; Coupling time constant (ps) ref_p= 1.0; Reference pressure for coupling, x-y, z directions (bar) compressibility = 4.5e-54.5e-5; Isothermal compressibility (bar^-1) refcoord_scaling = com Vacuum is incompatible with pressure coupling. Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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: Protein in vacum
Am I supposed to skip this step? Thanks for your reply. Sincerely, Shima ___ From: Dr. Vitaly Chaban To: gmx-us...@gromuracs.org Sent: Monday, January 28, 2013 3:17 PM Subject: [gmx-users] Re: Protein in vacum > > Dear users, > > I have done simulation with my protein in water earlier successfully using > CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the > last simulation of protein-water. When I go to the NPT equilibration, I get a > fatal error. > The commands I ran: > > The npt.mdp file settings are: > ; Parameters describing neighbors searching and details about interaction > calculations > ns_type = grid ; Neighbor list search method (simple, grid) > nstlist = 5 ; Neighbor list update frequency (after every given > number of steps) > rlist = 1.2 ; Neighbor list search cut-off distance (nm) > rlistlong = 1.4 > rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) > rvdw = 1.2 ; short-range van der Waals cutoff (in nm) > vdwtype = switch > rvdw_switch = 0.8 > ; Parameters for treating bonded interactions > continuation = no ; Whether a fresh start or a continuation from a > previous run (yes/no) > constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) > constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / > hbonds / none / all-angles / h-angles) > lincs_iter = 1 ; Number of iterations to correct for rotational > lengthening in LINCS (related to accuracy) > lincs_order = 4 ; Highest order in the expansion of the constraint > coupling matrix (related to accuracy) > > ; Parameters for treating electrostatic interactions > coulombtype = PME ; Long range electrostatic interactions treatment > (cut-off, Ewald, PME) > pme_order = 4 ; Interpolation order for PME (cubic interpolation is > represented by 4) > fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME > (nm) > > ; Temperature coupling parameters > tcoupl = Nose-Hoover ; Modified Berendsen thermostat using > velocity rescaling > tc-grps = Protein ; Define groups to be coupled separately to > temperature bath > tau_t = 0.5 ; Group-wise coupling time constant (ps) > ref_t = 310 ; Group-wise reference temperature (K) > > ; Pressure coupling parameters > pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT > conditions > pcoupltype = isotropic ; Isotropic scaling in the x-y > direction, independent of the z direction > tau_p = 5.0 ; Coupling time constant (ps) > ref_p = 1.0 ; Reference pressure for coupling, x-y, z > directions (bar) > compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility > (bar^-1) > refcoord_scaling = com Vacuum is incompatible with pressure coupling. Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- gmx-users mailing list gmx-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 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
