[gmx-users] Re: Viscosity calculation using cos_acceleration
Alternatively, has anyone else reproduced the viscosity calculation, or tried to? If anyone would be so kind as to forward their input files, that might help me narrow down the problem with my own input files. Thank you. James On 11 April 2013 16:55, James Cannon jamesresearch...@gmail.com wrote: Dear Gromacs users, This question seems to come up periodically in the mailing list, but none of the previous answers seem helpful in my case. I'm trying to reproduce the viscosity calculation of SPC water by Berk Hess (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get is 2 orders of magnitude out. My topology file and parameter file is appended at the bottom of this email. I run g_energy and get Energy Average Err.Est. RMSD Tot-Drift --- 1/Viscosity 23.4689 0.132.39126 -0.255371 (m s/kg) which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s The value quoted in the paper is about 0.4 mPa.s which is around the correct value for water, give or take a bit. So my question is, where is my missing factor of 100? Any advice is much appreciated. Thank you. James -- Topology file: #include ffgmx.itp #include spc.itp [ system ] Pure Water [ molecules ] SOL 3456 -- Parameter file for system (3456 SPC water molecules, 3.75x3.75x7.5 nm3 box): ;Generic mdp file for SPC water equilibration ;Gromacs 4.3.x ; ;T = 300 K ; ;NVT 1.2 ns ; define = ; define here posres etc., e.g. -DPOSRES integrator = md tinit = 0 dt = 0.001 nsteps = 120 ; Bond constraints continuation = no ; switch to 'yes' if need to read in velocities etc. constraints = none; constrain all bond lengths constraint_algorithm= lincs ; default lincs_order = 4 ; default nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file nstxtcout = 1000 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps= ; Selection of energy groups energygrps = System ; Neighbor list ns_type = grid; neighlist type nstlist = 5 ; Freq. to update neighbour list rlist= 0.9 ; nm (cutoff for short-range NL) pbc = xyz periodic_molecules = no ; Non-equilibrium MD ;acc_grps = SYSTEM cos_acceleration = 0.025 ; PPM option for viscosity calculation (nm/ps²) coulombtype = PME rcoulomb = 0.9 optimize_fft = yes ; affects only PME calculations ; if you use PME, set also rcoulomb = rlist ; van der Waals interactions vdwtype = Cut-off; Van der Waals interactions rvdw = 0.9; nm (LJ cut-off) DispCorr = EnerPres ; long-range dispersion correction to energy and pressure Tcoupl = berendsen tc-grps = System tau_t = 2.5 ref_t = 300.0 ;Pressure coupling Pcoupl = no gen_vel = no On 11 April 2013 16:55, James Cannon jamesresearch...@gmail.com wrote: Dear Gromacs users, This question seems to come up periodically in the mailing list, but none of the previous answers seem helpful in my case. I'm trying to reproduce the viscosity calculation of SPC water by Berk Hess (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get is 2 orders of magnitude out. My topology file and parameter file is appended at the bottom of this email. I run g_energy and get Energy Average Err.Est. RMSD Tot-Drift --- 1/Viscosity 23.4689 0.132.39126 -0.255371 (m s/kg) which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s The value quoted in the paper is about 0.4 mPa.s which is around the correct value for water, give or take a bit. So my question is, where is my missing factor of 100? Any advice is much appreciated. Thank you. James -- Topology file: #include ffgmx.itp #include spc.itp [ system ] Pure Water [ molecules ] SOL 3456 -- Parameter file for system (3456 SPC water molecules, 3.75x3.75x7.5 nm3 box): ;Generic mdp file for SPC water equilibration ;Gromacs 4.3.x ; ;T = 300 K ; ;NVT 1.2 ns ; define = ; define here
[gmx-users] Viscosity calculation using cos_acceleration
Dear Gromacs users, This question seems to come up periodically in the mailing list, but none of the previous answers seem helpful in my case. I'm trying to reproduce the viscosity calculation of SPC water by Berk Hess (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get is 2 orders of magnitude out. My topology file and parameter file is appended at the bottom of this email. I run g_energy and get Energy Average Err.Est. RMSD Tot-Drift --- 1/Viscosity 23.4689 0.132.39126 -0.255371 (m s/kg) which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s The value quoted in the paper is about 0.4 mPa.s which is around the correct value for water, give or take a bit. So my question is, where is my missing factor of 100? Any advice is much appreciated. Thank you. James -- Topology file: #include ffgmx.itp #include spc.itp [ system ] Pure Water [ molecules ] SOL 3456 -- Parameter file for system (3456 SPC water molecules, 3.75x3.75x7.5 nm3 box): ;Generic mdp file for SPC water equilibration ;Gromacs 4.3.x ; ;T = 300 K ; ;NVT 1.2 ns ; define = ; define here posres etc., e.g. -DPOSRES integrator = md tinit = 0 dt = 0.001 nsteps = 120 ; Bond constraints continuation = no ; switch to 'yes' if need to read in velocities etc. constraints = none; constrain all bond lengths constraint_algorithm= lincs ; default lincs_order = 4 ; default nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file nstxtcout = 1000 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps= ; Selection of energy groups energygrps = System ; Neighbor list ns_type = grid; neighlist type nstlist = 5 ; Freq. to update neighbour list rlist= 0.9 ; nm (cutoff for short-range NL) pbc = xyz periodic_molecules = no ; Non-equilibrium MD ;acc_grps = SYSTEM cos_acceleration = 0.025 ; PPM option for viscosity calculation (nm/ps²) coulombtype = PME rcoulomb = 0.9 optimize_fft = yes ; affects only PME calculations ; if you use PME, set also rcoulomb = rlist ; van der Waals interactions vdwtype = Cut-off; Van der Waals interactions rvdw = 0.9; nm (LJ cut-off) DispCorr = EnerPres ; long-range dispersion correction to energy and pressure Tcoupl = berendsen tc-grps = System tau_t = 2.5 ref_t = 300.0 ;Pressure coupling Pcoupl = no gen_vel = no -- 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] itp atomtypes section
Dear Tsjerk, Thanks for clarifying that for me. I appreciate it. Best regards, James On Tue, Nov 27, 2012 at 5:25 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi James, The 6 and 1 are the number of electrons the atomtype has, which is used for QM/MM stuff. Gromacs can tell whether or not it is given by checking the format of the line. If the 5th column is a letter, then the number isn't there, if the 6th column is a letter, it must be there. Hope it helps, Tsjerk On Tue, Nov 27, 2012 at 3:45 AM, James Cannon jamesresearch...@gmail.com wrote: Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 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] itp atomtypes section
Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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
