Re: [gmx-users] periodicity and correct output
Yes, mdrun applies PBC at every step and some atoms at top/bottom will translate to the bottom/top at some steps. So in dynamics simulation, the polarization given by gromacs is meaningless. Is there anyway I can apply PBC without translation ( e.g. change the box center automatically to avoid translation) ? Thanks, Shuangxing Dai On Wed, Jul 28, 2010 at 11:46 AM, Vitaly Chaban wrote: > Hi Shuangxing, > > For my case, I wrote a script just to do +/- LBOX when x>LBOX || x < > 0. I am not well familiar with polarization algorithm in gromacs but > it seems not to be a problem during a run since mdrun applies PBC at > every step. Maybe I am false here... > > Vitaly > > > On Wed, Jul 28, 2010 at 6:35 PM, Shuangxing Dai > wrote: > > I think I met the same problem. When apply periodicity to the system, > some > > atoms will translate to the other side of the box, and this gives wrong > > polarization values (especially in dynamic simulations). Anyone has idea > how > > to prevent this and get correct polarization in dynamics? > > Thanks, > > Shuangxing Dai > > > > > > On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban > wrote: > >> > >> Hi, > >> > >> Is there an option in any gromacs utility to apply periodicity to the > >> output configuration or trajectory? I want to get all the coordinates > >> just within an elementary box, between 0 and LBOX in spite of any > >> details of the system. > >> > >> For example, "editconf -no(pbc)" does not do its work since after > >> processing negative coordinates are sometimes present as well as those > >> bigger than LBOX. > >> > >> Vitaly > >> > >> Dr. Vitaly Chaban > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] periodicity and correct output
I think I met the same problem. When apply periodicity to the system, some atoms will translate to the other side of the box, and this gives wrong polarization values (especially in dynamic simulations). Anyone has idea how to prevent this and get correct polarization in dynamics? Thanks, Shuangxing Dai On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban wrote: > Hi, > > Is there an option in any gromacs utility to apply periodicity to the > output configuration or trajectory? I want to get all the coordinates > just within an elementary box, between 0 and LBOX in spite of any > details of the system. > > For example, "editconf -no(pbc)" does not do its work since after > processing negative coordinates are sometimes present as well as those > bigger than LBOX. > > Vitaly > > Dr. Vitaly Chaban > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] translation
Hi, all: I am running dynamics with PBC in xyz direction. Now I got a problem. Since PBC is applied, some atoms will move to the other side of the box and this will change the polarization. I need the results of polarization, so I do not hope that the polarization changed during the dynamics. Does anyone have idea how to solve this? Thanks in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] question about dynamics
Thanks for the help. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. Do you have any idea of this information? Thanks, Shuangxing Dai On Jul 12, 2010, at 15:43, "Justin A. Lemkul" wrote: > > > Shuangxing Dai wrote: >> Hi, all: >>I am studying thermal expansion of bulk crystal solid. I want to reach >> the state with 300K in temperature and 1 bar pressure. I am not sure >> whether my procedure is correct or not. >>First I run energy minimization, then a constant volume for temperature >> coupling ( integrator is sd), then run with Berendson for anisotropic >> pressure coupling for 50 ps, then run anisotropic pressure coupling using >> Panello-Rahman for 10 ps, finally a constant volume step for production for >> 10 ps. >>I do not know whether this procedure is correct or not. Also, since for >> my small system, fluctuation is very large, so is there any way to reach the >> state ( 300K and 1 bar) and the system is fully in equilibrium? > > The timeframes you're using are extremely short. I'd suspect that it would > be hard to get any system, especially a small one prone to large > fluctuations, in an equilibrium state in 70 ps total. Simple equilibration > of a protein in water is typically done for no less than 100 ps per ensemble. > >>Also, I got a question about the ,mdp file options. When I use md >> integrator, with Nose-Hover for temperature coupling and Panello-Rahman >> pressure coupling, there is no error information. When I change and use >> Berendson for pressure coupling, there is error information and does not >> work. > > Well, what's the error? This kind of description will get you no useful > advice. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. > > -Justin > >> Anyone have idea about these? Thanks in advance. >> Thanks, >> Shuangxing Dai > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] question about dynamics
Hi, all: I am studying thermal expansion of bulk crystal solid. I want to reach the state with 300K in temperature and 1 bar pressure. I am not sure whether my procedure is correct or not. First I run energy minimization, then a constant volume for temperature coupling ( integrator is sd), then run with Berendson for anisotropic pressure coupling for 50 ps, then run anisotropic pressure coupling using Panello-Rahman for 10 ps, finally a constant volume step for production for 10 ps. I do not know whether this procedure is correct or not. Also, since for my small system, fluctuation is very large, so is there any way to reach the state ( 300K and 1 bar) and the system is fully in equilibrium? Also, I got a question about the ,mdp file options. When I use md integrator, with Nose-Hover for temperature coupling and Panello-Rahman pressure coupling, there is no error information. When I change and use Berendson for pressure coupling, there is error information and does not work. Anyone have idea about these? Thanks in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] pressure coupling
Thanks for the response. Yes, I know that large fluctuations will be expected. But why the average was not even correct? Also, how can I reach some state ( some pressre and temperature) and know/tell that the system is in equilibrium if the average is not correct with large fluctuation? I mean I do not know the criteria of Gromacs. Or maybe my procedure is wrong? Message: 1 Date: Mon, 05 Jul 2010 10:39:30 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] pressure coupling To: Discussion list for GROMACS users Message-ID: <4c31eea2.7070...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Shuangxing Dai wrote: > Hi, all, > I am trying to do anisotropic coupling using Parrinello-Rahman. I > want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, > I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, > fluctuation is 626 bar for pressure and 11.21 K for temperature.) I run > energy minimization first, then Berenderson pressure coupling for 50 ps, > finally Parrinello-Rahman pressure coupling for 50 ps. Anyone has > experience on anisotropic coupling and know why? > My system has just 4000 atoms. This is my .mdp file: > For a small system, large fluctations in the pressure are to be expected: http://www.gromacs.org/Documentation/Terminology/Pressure -Justin > ;define = -DPOSRES > ; RUN CONTROL PARAMETERS = > integrator = sd > ; start time and timestep in ps = > tinit= 0 > dt = 0.001 > nsteps = 5 > ; number of steps for center of mass motion removal = > nstcomm = 100 > ; OUTPUT CONTROL OPTIONS = > ; Output frequency for coords (x), velocities (v) and forces (f) = > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Output frequency for energies to log file and energy file = > nstlog = 10 > nstenergy= 10 > ; Output frequency and precision for xtc file = > nstxtcout= 10 > xtc-precision= 1000 > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 20 > ; ns algorithm (simple or grid) = > ns_type = grid > > ;OPTIONS FOR PRESSURE COUPLING > Pcoupl = Parrinello-Rahman > pcoupltype = anisotropic > tau_p= 5 > compressibility = 2.1645e-07 2.1645e-07 2.7322e-07 0 0 0 > ref_p= 1 1 1 0 0 0 > ;OPTIONS FOR TEMPERATURE COUPLING > tc_grps = system > tau_t= 1 > ref_t= 1000 > ; OPTIONS FOR BONDS = > constraints = hbonds > ; Type of constraint algorithm = > constraint-algorithm = Lincs > ; Do not constrain the start configuration = > unconstrained-start = no > ; Relative tolerance of shake = > shake-tol= 0.0001 > ; Highest order in the expansion of the constraint coupling matrix = > lincs-order = 12 > ; Lincs will write a warning to the stderr if in one step a bond = > ; rotates over more degrees than = > lincs-warnangle = 30 > ; Periodic boundary conditions: xyz, no, xy > pbc = xyz > periodic_molecules = no > ; nblist cut-off > rlist= 1 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME > rcoulomb = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw = 1 > > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order= 6 > ewald_rtol = 1e-4 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > > > > I used the same procedure to reach different state ( like 0.01 K, 100K, > 300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average > pressure and small fluctuation. > T p(bar) delta p T (K) delta T > 0.01 1.03E+002.12E+009.95E-031.21E-04 > 100 5.48359 71.5565 91.198 1.25218 > 300 2.62807 162.926 290.324 3.36594 > 500 16.6356 1048.76 492.616 5.45231 > 800 59.3245 594.773 799.314 9.18876 > 1000 80.2257 626.789 1007.23 11.2159 > > Thanks in advance,
[gmx-users] pressure coupling
Hi, all, I am trying to do anisotropic coupling using Parrinello-Rahman. I want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, fluctuation is 626 bar for pressure and 11.21 K for temperature.) I run energy minimization first, then Berenderson pressure coupling for 50 ps, finally Parrinello-Rahman pressure coupling for 50 ps. Anyone has experience on anisotropic coupling and know why? My system has just 4000 atoms. This is my .mdp file: ;define = -DPOSRES ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file = nstxtcout= 10 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 20 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = Parrinello-Rahman pcoupltype = anisotropic tau_p= 5 compressibility = 2.1645e-07 2.1645e-07 2.7322e-07 0 0 0 ref_p= 1 1 1 0 0 0 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 1 ref_t= 1000 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no I used the same procedure to reach different state ( like 0.01 K, 100K, 300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average pressure and small fluctuation. T p(bar) delta p T (K) delta T 0.01 1.03E+00 2.12E+00 9.95E-03 1.21E-04 100 5.48359 71.5565 91.198 1.25218 300 2.62807 162.926 290.324 3.36594 500 16.6356 1048.76 492.616 5.45231 800 59.3245 594.773 799.314 9.18876 1000 80.2257 626.789 1007.23 11.2159 Thanks in advance, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 84
Well, the final average pressure is not correct: * **<== ### ==>* * **< A V E R A G E S >* * **<== ### ==>* * * * Energies (kJ/mol)* * Buck.ham (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. * *1.60633e+06 -5.69243e+06 -3.45003e+06 -7.53612e+061.80719e+04 * * Total EnergyTemperature Pressure (bar)* * -7.51805e+063.62347e+021.11758e+04* * * * * * Pressure (bar)* *1.21051e+04 -2.94017e-011.30456e+00* * -2.94017e-019.03597e+03 -8.10850e-01* *1.30456e+00 -8.10850e-011.23863e+04* * * * * * **<== ### ==>* * **< R M S - F L U C T U A T I O N S >* * **<== ### ==>* * * * Energies (kJ/mol)* * Buck.ham (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. * *3.92376e+054.00326e+054.71365e+013.02978e+042.35039e+03 * * Total EnergyTemperature Pressure (bar)* *3.01091e+044.71259e+011.71117e+05* * * * * * Pressure (bar)* *1.82323e+054.91513e+023.07107e+02* *4.91513e+022.02402e+053.13857e+02* *3.07107e+023.13857e+021.30179e+05* * * *Also the fluctuation is very large. I think 200ps is long enough. But still I cannot find the equilibrium.* *I do not know whether the parameters are wrong or I ran the anisotropic pressure coupling wrong. Is *Parrinello-Rahman pressure coupling sensitive to the initial pressure? I mean if the initial pressure ( in order of GPa), object pressure is 1 bar ( 1e5 Pa). * * Thanks, Shuangxing Dai On Mon, Jun 14, 2010 at 8:50 PM, wrote: > > > Message: 3 > Date: Mon, 14 Jun 2010 19:18:14 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] anisotropic pressure coupling > To: Discussion list for GROMACS users > Message-ID: <4c16b8b6.4010...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Shuangxing Dai wrote: > > Hi all: > > I was using Parrinello-Rahman for pressure coupling and here is the > > mdp file: > > > > ; RUN CONTROL PARAMETERS = > > integrator = sd > > ; start time and timestep in ps = > > tinit= 0 > > dt = 0.001 > > nsteps = 20 > > ; number of steps for center of mass motion removal = > > nstcomm = 100 > > ; NEIGHBORSEARCHING PARAMETERS = > > ; nblist update frequency = > > nstlist = 50 > > ; ns algorithm (simple or grid) = > > ns_type = grid > > > > ;OPTIONS FOR PRESSURE COUPLING > > Pcoupl = Parrinello-Rahman > > pcoupltype = anisotropic > > tau_p= 1 > > compressibility = 2.1645e-09 2.1645e-09 2.7322e-09 0 0 0 > > ref_p= 1 1 1 0 0 0 > > ;OPTIONS FOR TEMPERATURE COUPLING > > tc_grps = system > > tau_t= 0.1 > > ref_t= 300 > > ; OPTIONS FOR BONDS = > > constraints = hbonds > > ; Type of constraint algorithm = > > constraint-algorithm = Lincs > > ; Do not constrain the start configuration = > > unconstrained-start = no > > ; Relative tolerance of shake = > > shake-tol= 0.0001 > > ; Highest order in the expansion of the constraint coupling matrix = > > lincs-order = 12 > > ; Lincs will write a warning to the stderr if in one step a bond = > > ; rotates over more degrees than = > > lincs-warnangle = 30 > > ; Periodic boundary conditions: xyz, no, xy > > pbc = xyz > > periodic_molecules = no > > ; nblist cut-off > > rlist= 1 > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = PME > > rcoulomb = 1 > > ; Method for doing Van der Waals > > vdw-type = Cut-off > > ; cut-off lengths > > rvdw = 1 > > > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; FFT grid size, when a value is 0 fourierspacing will be used > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > ; EWALD/PME/PPPM parameters > > pme_order= 6 > > ewald_rtol = 1e-4 > > ewald_geometry = 3d > > epsilon_surface = 0 > > optimize_fft = no > > > > It seems that the temperature couplin
[gmx-users] anisotropic pressure coupling
Hi all: I was using Parrinello-Rahman for pressure coupling and here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = Parrinello-Rahman pcoupltype = anisotropic tau_p= 1 compressibility = 2.1645e-09 2.1645e-09 2.7322e-09 0 0 0 ref_p= 1 1 1 0 0 0 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 300 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no It seems that the temperature coupling is fast and fluctuation is less that 1%. But the pressure coupling fails. The pressure fluctuates from +1e3 bar to -1e3 bar. Anyone can help? Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: anisotropic pressure coupling
|> Hi, all: |>I was trying to use pcoupl= Parrinello-Rahman, pcouptype=anisotropic |> to do pressure coupling for anisotropic material (like crystal). It |> seems that I need six components for compressibility (xx yy zz xy yz |> xz). How do I get these six components before I do any MD simulation? | |Surely there are published results that you can refer to for these types of |considerations. Well, anyone used anisotropic pressure coupling in gromacs can share a link of literature which contains those compressibility components they can use and used in gromacs? I have no idea how the all the components compressibility be calculated ( for my wurtzite crystal) and used in gromacs to conduct a anisotropic pressure coupling. Any shared experience will be appropriated. |> Also, if the compressibility changes with temperature and pressure, how |> can we use a fixed value of compressibility to simulate a system that |> changes from one state to another? Or the compressibility is not so |> sensitive to temperature and pressure? | |You can change temperature with simulated annealing, but how do you expect to |modulate the pressure? There's no way to systematically alter the pressure. If |your goal is to alter these factors somehow, then you have a very complicated |situation, and there is no really easy way to do it. You may have to do |different simulations under different conditions using known compressibilities. | |> Anyone has experience in using Parrinello-Rahman? Thanks in advance. | |Sure, many people do. What is it that you want to know about it? | |-Justin > Thanks, > Shuangxing Dai > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
[gmx-users] anisotropic pressure coupling
Hi, all: I was trying to use pcoupl= Parrinello-Rahman, pcouptype=anisotropic to do pressure coupling for anisotropic material (like crystal). It seems that I need six components for compressibility (xx yy zz xy yz xz). How do I get these six components before I do any MD simulation? Also, if the compressibility changes with temperature and pressure, how can we use a fixed value of compressibility to simulate a system that changes from one state to another? Or the compressibility is not so sensitive to temperature and pressure? Anyone has experience in using Parrinello-Rahman? Thanks in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: slow speed
I am not running in parallel. Right now I just changed links order from 12 to 4. It is still slow. While I change to shift, not Ewald, it finished 1 steps in 10 mins. In the paper: J Comput Chem. 2005 Dec;26(16):1701-18. GROMACS: fast, flexible, and free.<http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.103.418&rep=rep1&type=pdf> Van Der Spoel D<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Van%20Der%20Spoel%20D%22%5BAuthor%5D> , Lindahl E<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lindahl%20E%22%5BAuthor%5D> , Hess B<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Hess%20B%22%5BAuthor%5D> , Groenhof G<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Groenhof%20G%22%5BAuthor%5D> , Mark AE<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Mark%20AE%22%5BAuthor%5D> , Berendsen HJ<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Berendsen%20HJ%22%5BAuthor%5D> . The performance there is around 1 ps/day. I do not understand why my speed is so slow and it seems that Ewald option makes it slow. Thanks, Shuangxing Dai On Thu, Apr 15, 2010 at 10:18 AM, wrote: > Send gmx-users mailing list submissions to >gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit >http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to >gmx-users-requ...@gromacs.org > > You can reach the person managing the list at >gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. slow speed (Shuangxing Dai) > 2. Re: slow speed (Justin A. Lemkul) > 3. Re: slow speed (XAvier Periole) > 4. Re: slow speed (Mark Abraham) > > > -- > > Message: 1 > Date: Thu, 15 Apr 2010 10:02:47 -0400 > From: Shuangxing Dai > Subject: [gmx-users] slow speed > To: gmx-users@gromacs.org > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi, gmx-users: > I am using latest version of gromacs and found it was really slow. I was > wondering anyone got the same experience and can point out where the > problem > is. > I was running double precision for MD. But for each dynamics simulation, > it takes 4 days. I should only take two or three hours. > Here is the .mdp file: > define = > ; RUN CONTROL PARAMETERS = > integrator = sd > ; start time and timestep in ps = > tinit= 0 > dt = 0.001 > nsteps = 20 > ; number of steps for center of mass motion removal = > nstcomm = 100 > ; OUTPUT CONTROL OPTIONS = > ; Output frequency for coords (x), velocities (v) and forces (f) = > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Output frequency for energies to log file and energy file = > nstlog = 100 > nstenergy= 100 > ; Output frequency and precision for xtc file = > nstxtcout= 100 > xtc-precision= 1000 > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 50 > ; ns algorithm (simple or grid) = > ns_type = grid > > ;OPTIONS FOR PRESSURE COUPLING > Pcoupl = berendsen > tau_p= 1 > compressibility = 4.5e-05 > ref_p= 0.1 > ;OPTIONS FOR TEMPERATURE COUPLING > tc_grps = system > tau_t= 0.1 > ref_t= 300 > ; OPTIONS FOR BONDS = > constraints = hbonds > ; Type of constraint algorithm = > constraint-algorithm = Lincs > ; Do not constrain the start configuration = > unconstrained-start = no > ; Relative tolerance of shake = > shake-tol= 0.0001 > ; Highest order in the expansion of the constraint coupling matrix = > lincs-order = 12 > ; Lincs will write a warning to the stderr if in one step a bond = > ; rotates over more degrees than = > lincs-warnangle = 30 > ; Periodic boundary conditions: xyz, no, xy > pbc = xyz > periodic_molecules = no > ; nblist cut-off > rlist= 1 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = Ewald > rcoulomb = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw = 1 > > ; Spacing for the PME/P
[gmx-users] slow speed
Hi, gmx-users: I am using latest version of gromacs and found it was really slow. I was wondering anyone got the same experience and can point out where the problem is. I was running double precision for MD. But for each dynamics simulation, it takes 4 days. I should only take two or three hours. Here is the .mdp file: define = ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 1 compressibility = 4.5e-05 ref_p= 0.1 ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 300 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald rcoulomb = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-4 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Can anyone help me? Thank you in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Does shell molecular exclude core shell electrostatics automatically
Hi, all, I was wondering if the shell molecular dynamics exclude the electrostatic interaction automatically. According to the shell model, the interaction between core and shell in replaced by the harmonic interaction. If not, how to exclude electrostatic interaction between them? If I define in the top file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 21 no 1.0 1.0 [ atomtypes ] ;name at.num masscharge ptype a b c O815.99940 0.040 A 0.0E-00 0.0E-00 0.0E-00 OS80.0 -2.040 S 0.0E-00 0.0E-00 0.0E-00 ZN 30 65.37000 2.000 A 0.0E-00 0.0E-00 0.0E-00 [ nonbond_params ] ; ij func a bc OS OS2 9.21239E+05 4.56287E+01 3.08753E-03 OS ZN2 5.11083E+04 2.79251E+01 0.0E+00 ZN ZN2 0.0E+00 1.0E+02 0.0E+00 OS is shell and O is core for oxygen. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] use Xcode to debug Gromacs
Dear all, I was trying to use Xcode to debug the file mdrun and hope to trace the flow of source file by running a simple case. There is a tutorial for using Xcode to debug a package named apbs, which is very like Gromacs, here: http://www.macresearch.org/tutorial-introducing-xcode-30-organizer I followed the tutorial and it works well for apbs. But when I did the same thing for Gromacs, I can only see the assemble code for mdrun and it was not connected to the source code. Only assemble code does not help. So my question is: anyone know how to use Xcode to debug Gromacs executable file? I need the breakpoints to be related with the source code so that I can trace the flow. Sorry for the last mail that I pressed space accidently... Thank you in advance. -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] use Xcode to debug Gromacs
Dear all, -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] how to debug a single executable file using Xcode
Dear all, I was wondering how to debug the executable file mdrun in Xcode. Right now I can debug it using gdb by following here: http://oldwiki.gromacs.org/index.php/Programmer's_Guide But I do not know how to debug it by Xcode. For example, I want to debug this command: mdrun -c steep.g96 Right now I know how to debug a source code and the executable file generated by this code. But I have no idea how to debug this single executable file using Xcode. I am trying to do is to understand how the mdrun works in one example. So anyone can help me? Thanks in advance. Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] large pressure
Hi, all, I was wondering why I got large pressure after energy minimization. In MD, the pressure and pressure tensor is defined like ( equation 4.151 in manual): P=2*(E_kinetic + W)/(3*V), V is volume and W is Virial. I run a simple system, fcc gold with LJ potential to check the pressure after energy minimization. I got: Pressure (bar) 8.75158e+03 Steepest Descents converged to Fmax < 1 in 1 steps Potential Energy = -1.4870625e+03 Maximum force = 2.2925207e-05 on atom 1606 Norm of force = 7.9803776e-06 The force is very small and the energy minimization finished in 1 steps, since all the atoms are at equilibrium. So I was wondering why I got this huge pressure. And in a lot of simulations, I found huge pressure after energy minimization. Even in free energy tutorial on Wiki, I found large pressure as larege as 1 GPa. After energy minimization, the forces are very small and no velocity, so the pressure should be close to zero. Anyone has any idea about this? PS: Why the forces in traj.trr are all zeros? This is the mdp file: ; RUN CONTROL PARAMETERS = integrator = steep nsteps = 500 ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file = nstlog = 1 nstenergy= 1 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 1 emstep = 0.01 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 1 ; ns algorithm (simple or grid) = ns_type = simple ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths= rvdw = 0.9 Thanks in advance, Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Shift electrostatic summation
Dear all, I was trying to modify the Shift option of electrostatic summation. Mainly I want to modify the formulas of this electrostatic summation. From the manual page 69, the modified non-bonded interactions, the formulas about Shift is there. In the file /src/gmxlib/shift_util.c, there are these formulas. So is this the only file for Shift? Since I have added some printf lines to this file, I do not see the result when I recompile and use Shift. I doubt whether this function was called to do Shift. Or is there any other file related with the Shift method and I need to change? Thanks in advance. -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] force
Yes, I did one md step and got all non-zero forces. But for the energy minimization, all the forces are zero, althouth mdrun command gives non-zero forces. On Sun, Jun 28, 2009 at 4:23 AM, Florian Dommert < domm...@icp.uni-stuttgart.de> wrote: > * Shuangxing Dai [2009-06-27 20:22:13 -0600]: > > Yes, they are all zeros. I am confused why this happen. Thank you for >> help. >> And here is the mdp file: >> > > That would confuse me, too. As I have never analyzed forces from a > energy minimization, perhaps there is the problem. Try a zero-step md, > meaning integrator=md and nsteps=0 and leave the further parameters > unchanged. In case you get forces in your analysis then, we have > discovered the source of error :) > > /Flo > > ; RUN CONTROL PARAMETERS = >> integrator = steep >> nsteps = 50 >> ; Output frequency for coords (x), velocities (v) and forces (f) >> nstxout = 1 >> nstvout = 1 >> nstfout = 1 >> ; Output frequency for energies to log file and energy file >> nstlog = 1 >> nstenergy= 1 >> ; Output frequency and precision for xtc file >> nstxtcout= 1 >> xtc-precision= 1000 >> ; ENERGY MINIMIZATION OPTIONS = >> ; Force tolerance and initial step-size = >> emtol= 1 >> emstep = 0.01 >> ; NEIGHBORSEARCHING PARAMETERS = >> ; nblist update frequency = >> nstlist =3 >> ; ns algorithm (simple or grid) = >> ns_type = simple >> ; Periodic boundary conditions: xyz or none = >> pbc = xyz >> ; nblist cut-off = >> rlist=0.9 >> ; OPTIONS FOR ELECTROSTATICS AND VDW = >> ; Method for doing electrostatics = >> coulombtype = Shift >> rcoulomb = 0.9 >> ; Dielectric constant (DC) for cut-off or DC of reaction field = >> epsilon-r= 1 >> ; Method for doing Van der Waals = >> vdw-type = Cut-off >> ; cut-off lengths= >> rvdw = 0.9 >> ; Spacing for the PME/PPPM FFT grid = >> fourierspacing = 0.1 >> ; FFT grid size, when a value is 0 fourierspacing will be used = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters = >> pme_order= 6 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> >> And also another question, can Gromacs write out the energy for each atom >> at >> each step? Just like it did to the forces? I use this mdp file and only >> see >> the total energy for each step in the log file. >> Thanks again. >> >> On Sat, Jun 27, 2009 at 8:07 PM, Florian Dommert < >> domm...@icp.uni-stuttgart.de> wrote: >> >> * Shuangxing Dai [2009-06-27 18:57:41 -0600]: >>> >>> The nstfout =1 in mdout.mdp. So this should not be where the problem is. >>> >>>> >>>> >>> So this was the most obvious mistake I could imagine and you see it is >>> always appreciated that you put your mdp file also to the list, that >>> everybody knows your input parameters. However in case you already told >>> gromacs to write out the data to the trr file it should be there. >>> So if you try: >>> >>> echo 0 | g_traj -f traj.trr -s topol.tpr -of >>> Only zeros are contained in force.xvg ?? >>> >>> /Flo >>> >>> >>> >>> - Original Message - From: "Florian Dommert" < >>>> domm...@icp.uni-stuttgart.de> >>>> To: "Discussion list for GROMACS users" >>>> Sent: Saturday, June 27, 2009 3:20 PM >>>> Subject: Re: [gmx-users] force >>>> >>>> >>>> ___ >>>> >>>>> gmx-users mailing listgmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>>>> >>>>>
Re: [gmx-users] force
Yes, they are all zeros. I am confused why this happen. Thank you for help. And here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = steep nsteps = 50 ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1 ; Output frequency and precision for xtc file nstxtcout= 1 xtc-precision= 1000 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 1 emstep = 0.01 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist =3 ; ns algorithm (simple or grid) = ns_type = simple ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist=0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths= rvdw = 0.9 ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no And also another question, can Gromacs write out the energy for each atom at each step? Just like it did to the forces? I use this mdp file and only see the total energy for each step in the log file. Thanks again. On Sat, Jun 27, 2009 at 8:07 PM, Florian Dommert < domm...@icp.uni-stuttgart.de> wrote: > * Shuangxing Dai [2009-06-27 18:57:41 -0600]: > > The nstfout =1 in mdout.mdp. So this should not be where the problem is. >> > > So this was the most obvious mistake I could imagine and you see it is > always appreciated that you put your mdp file also to the list, that > everybody knows your input parameters. However in case you already told > gromacs to write out the data to the trr file it should be there. > So if you try: > > echo 0 | g_traj -f traj.trr -s topol.tpr -of > Only zeros are contained in force.xvg ?? > > /Flo > > > >> - Original Message - From: "Florian Dommert" < >> domm...@icp.uni-stuttgart.de> >> To: "Discussion list for GROMACS users" >> Sent: Saturday, June 27, 2009 3:20 PM >> Subject: Re: [gmx-users] force >> >> >> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > Florian Dommert > Dipl.-Phys. > > Institute for Computational Physics > University Stuttgart > > Pfaffenwaldring 27 > 70569 Stuttgart > > Tel: +49 - 711 / 6856-3613 > Fax: +49 - 711 / 6856-3658 > > EMail: domm...@icp.uni-stuttgart.de > Home: > http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert<http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert> > > !! PGP-ENCODED emails preferred !! > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] force
The nstfout =1 in mdout.mdp. So this should not be where the problem is. - Original Message - From: "Florian Dommert" To: "Discussion list for GROMACS users" Sent: Saturday, June 27, 2009 3:20 PM Subject: Re: [gmx-users] force ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] force
Hi, all,
I was wondering about the force given by Gromacs. One is in the .trr and
.tpr file. When I read then with gmxdump, they are all zeros:
traj.trr frame 0:
natoms= 24000 step= 0 time=0.000e+00 lambda= 0
box (3x3):
box[0]={ 3.24900e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 5.62743e+00, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 1.04120e+01}
f (24000x3):
f[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
f[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
f[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
f[3]={ 0.0e+00, 0.0e+00, 0.0e+00}
When I use mdrun -pforce 0 to get all the non-zero force, I get:
step 0 atom 4687 x0.9753.1890.781 force 3.58158e+02
step 0 atom 4688 x0.9753.1890.586 force 7.16316e+00
step 0 atom 4689 x0.9753.1890.586 force 3.65324e+02
step 0 atom 4690 x0.8123.0951.041 force 3.58167e+02
step 0 atom 4691 x0.8123.0950.846 force 7.16314e+00
Why this happens? Thanks in advance.
Shuangxing Dai___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] more digits
Hi, all, I need more digits to input information. But the default format of pdb file for coordinate is %8.3f. Can I modify the pdbio.c file to achive this goal? Or is there any other direct ways to input more digits coordinate information in Gromacs? Thanks in advance. Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Shift Electrostatic Summation
Thank you for your advice and sorry for the misinterpretation. The N is the total number of the system and E^Mad_tot is the total energy for the system. The outer loop sums over all the ions and the inner one sums over the neighbours in the cut-off radius. So it is difficult to decompose this total energy to the summation of pair potential since the self energy part is not easy to decompose. I will follow your advice. Thanks again. Shuangxing Dai - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 10:21 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 8:01 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. The number of neighbours is known at run-time. However, I still don't see why this matters - see http://www.gromacs.org/pipermail/gmx-users/2009-March/040830.html OK, the self energy is assigned for each ion. If I want to decompose the potential form of total energy to summation of pair potential, I should devide the self term by number of neighbours and assigned to each pair. So I cannot use user define potential for my problem. You can use a user potential if the dependence of the force and/or potential on r and N is sufficiently separable. The number of neighbours is known inside the inner nonbonded loops, because they're looping over the neighbours of each particle. So you merely do a table lookup before or after some function of N is applied to some function of r. Thus the only work you'd need to do is to construct the correct form of tables, and add in the arithmetic concerning N. Per my advice in that previous thread, you should read and understand the code for the nonbonded kernel for a straight cutoff, compare that with non-table-lookup Ewald, and compare that with table-lookup Ewald. Also heed the advice Berk gave you. You've still never explained why N in the formula in that previous thread is the number of neighbours of a given particle, not the number of particles in the system - but that's your problem. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Shift Electrostatic Summation
- Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 8:01 PM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. The number of neighbours is known at run-time. However, I still don't see why this matters - see http://www.gromacs.org/pipermail/gmx-users/2009-March/040830.html OK, the self energy is assigned for each ion. If I want to decompose the potential form of total energy to summation of pair potential, I should devide the self term by number of neighbours and assigned to each pair. So I cannot use user define potential for my problem. And I cannot understand/find how the force for Shift electrostatic summation is calculated in force.c since there is no formula for force found. Or I find the wrong place? And if I want to modify the force formula for Shift, where is it? Look in the nonbonded kernels - like I said in the above post and previously. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Shift Electrostatic Summation
Thank you for your help. Yes, when I found the user define part for electrostatics, I hope I can use this part since the analytic form of my potential is known. However, since there is a self energy term exist and then the whole energy cannot be decomposed to pair interactions because I cannot specify how much to each pair since the number of neighbours is unkown. That is why I am confused. So I still need an new electrostatic summation similiar to shift, not just a new pair interaction. And I cannot understand/find how the force for Shift electrostatic summation is calculated in force.c since there is no formula for force found. Or I find the wrong place? And if I want to modify the force formula for Shift, where is it? Thank you for your help. Shuangxing Dai - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 14 April, 2009 12:46 AM Subject: Re: [gmx-users] Shift Electrostatic Summation Shuangxing Dai wrote: Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( something like that ), I need to q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is: How the force to Shift was calculated? Gromacs use the differentiation to energy, got the force formula, then calculated the force? Or just use the numerical differentiation to the energy and got it? If is the latter one, I do not need to modify the force calculation. GROMACS uses exclusively analytic rather than numerical forces. Probably table lookups as used for PME are the technique you will want to implement. You won't need to change any code if your functions are suitably continuous functions of r and constant parameters. See the tabulated potentials section in the manual. And also, the alpha for Ewald summation, is there an option or parameters to adjust this value? Yes - see the Ewald section of the manual. Also search the mailing list, as this has been discussed several times. Hi, Mark and Berk, if I want do modify shift electrostatic summation as I want, what other files or place do I need to modify, except shift_util.c and force.c? Don't - use table lookups. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Shift Electrostatic Summation
Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( something like that ), I need to q^2*(erfc(alpha*Rc)/(2*Rc)+alpha/sqrt(pi)). So question is: How the force to Shift was calculated? Gromacs use the differentiation to energy, got the force formula, then calculated the force? Or just use the numerical differentiation to the energy and got it? If is the latter one, I do not need to modify the force calculation. And also, the alpha for Ewald summation, is there an option or parameters to adjust this value? Hi, Mark and Berk, if I want do modify shift electrostatic summation as I want, what other files or place do I need to modify, except shift_util.c and force.c? Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] shell molecular dynamics
Thank you for help. The harmonic potential between core and shell is attractive. The charges they have are opposite, this means that there will only be attractive force between them. My result also show that they nearly overlap. Is this reasonable and shell model correctly used? If not, where is the problem. Shuangxing Dai - Original Message - From: "David van der Spoel" To: "Discussion list for GROMACS users" Sent: 13 April, 2009 11:15 AM Subject: Re: [gmx-users] shell molecular dynamics Shuangxing Dai wrote: Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell "atom", what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? Anything you like. Gromacs does not use this information anyway. 2. What does the 1 in [ polarization ] part mean in sw.itp? Function type, see manual ch. 5. 3. Is it reasonable to set initial position of shell arbitrally and let energy minimization to find the optimum position for shell? At first step the shell will be put in the place of the virtual site and will be minimized from there. I also do not understand [ exclusion ] part: ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 For the first line, does that mean that the interaction of 2, 3, 4 and 5 with 1 is excluded? If so, this table will exclude all the interactions. Is it right? Yes. You need at least two molecules to do anything useful. Thank you in advance. Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] shell molecular dynamics
Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell "atom", what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? 2. What does the 1 in [ polarization ] part mean in sw.itp? 3. Is it reasonable to set initial position of shell arbitrally and let energy minimization to find the optimum position for shell? I also do not understand [ exclusion ] part: ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 For the first line, does that mean that the interaction of 2, 3, 4 and 5 with 1 is excluded? If so, this table will exclude all the interactions. Is it right? Thank you in advance. Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to add another electrostatic summation methodinGromacs
- Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 27 March, 2009 5:01 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodinGromacs Shuangxing Dai wrote: Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot use the user defined part to do my eletrostatic summation. If N is the number of neighbours inside the cutoff distance, then you might be right. If so, then I don't understand why the inner summation constrains "j != i" and "r_ij < R_c" since the latter is implied by formation of the set over which the summations are occurring. If N is the total number of ions then the last few terms are all system-wide constants. Sorry, (5.13) is the total electrostatic potential energy for the system and the N is the total number of ions. I also don't understand why the limit expression exists. For any values actually used in a simulation, that expression is just a constant. In simulation, we simply uses r_ij = R_c, so ignore the limit. I compared carefully with Wolf summation with the Ewald summation, the differences are: 1. There is no reciprocal term in Wolf. 2.Instead, the Wolf assums that the ions out side the truncations sphere is exactly located at the sphere. That is how the extra two terms come out. The second and third terms came from this treatment. 3. Wolf uses cut-off, while Ewald can only deal with peoriodical boundary conditions cases. So I need to add a similiar summation like Ewald to treat with the long-range electrostatic force, not a non-bonded interaction. Then which parts needs to be read and modified? I don't understand your conclusion, here. OK. I mean I need to add a eletrostatic summation method very similiar to Ewald. So where is definition/algorithm of Ewald in Gromacs and how to add one? Thank you for your kind help. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to add another electrostatic summation methodin Gromacs
Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot use the user defined part to do my eletrostatic summation. I compared carefully with Wolf summation with the Ewald summation, the differences are: 1. There is no reciprocal term in Wolf. 2.Instead, the Wolf assums that the ions out side the truncations sphere is exactly located at the sphere. That is how the extra two terms come out. 3. Wolf uses cut-off, while Ewald can only deal with peoriodical boundary conditions cases. So I need to add a similiar summation like Ewald to treat with the long-range electrostatic force, not a non-bonded interaction. Then which parts needs to be read and modified? Thank you for your kindly help. Shuangxing Dai - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 26 March, 2009 4:56 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodin Gromacs Shuangxing Dai wrote: Thank you for your help. I attached the page of the form of potential. The equation (5.13) gives all the potential energy of neighbours of one ion in a truncation sphere. Rc is cut-off. Since this potential depends on all the neighbours in a cut-off distance, I cannot give the pair interaction because in this method, only the total potential energy of one ion maks sense. In Ewald summation, both the real space and reciprocal space summation can be written as the summation of pair potential. But in wolf, I cannot do that. It looks separable into a double sum over atom pairs from within a cutoff, since the value of that limit is constant. Since I cannot use Ewald without peoriodical boundary conditions while this Wolf method can, so I cannot simply use Gromacs to do my simulation. The question is which files needed to be modified if I want to add a new one? Is there any direct way? Or I should read all the whole code? You can start by reading the kernel code generated by mknb during the make process and found in src/gmxlib/nonbonded/nb_kernel. If you play with the flags to mknb you can get comments embedded in the C files. Find the one that does Ewald without table lookups and consider how you'd need to change it to suit your needs. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to add another electrostatic summation method in Gromacs
Thank you for your help. I attached the page of the form of potential. The equation (5.13) gives all the potential energy of neighbours of one ion in a truncation sphere. Rc is cut-off. Since this potential depends on all the neighbours in a cut-off distance, I cannot give the pair interaction because in this method, only the total potential energy of one ion maks sense. In Ewald summation, both the real space and reciprocal space summation can be written as the summation of pair potential. But in wolf, I cannot do that. Since I cannot use Ewald without peoriodical boundary conditions while this Wolf method can, so I cannot simply use Gromacs to do my simulation. The question is which files needed to be modified if I want to add a new one? Is there any direct way? Or I should read all the whole code? Thank you very much. Shuangxing Dai On Mon, Mar 23, 2009 at 11:55 PM, Mark Abraham wrote: > Shuangxing Dai wrote: > >> Hi, all, >>I was wondering how to add another electrostatic summation method--Wolf >> summation into Gromacs. Wolf summation is a treatment for summation of >> Coulombic energy. Since the formula of total potential energy for each ion >> is known, how to add this into Gromacs? According to Chapter 7, I should >> give the f(x) and f'(x). The formula of f and f' depends on the neighbours >> and varies from ion to ion, and I can not give f and f' without calculation. >> > > If you have a functional form that depends only on pairwise distance and > two atom types, then you can use the GROMACS table lookup machinery. > > Since Wolf method uses the same error function as Ewald summation, it might >> be easier and possible to implement Wolf into Gromacs. If so, which files >> need to be modified? >> Hope I put my question clearly. Thank you in advance for suggestions and >> help. >> > > Evaluating erfc is not the core issue - but GROMACS does the evaluation of > terms for the direct-space Ewald contribution via table-lookup. The big deal > is whether you need a custom non-bonded kernel, and then whether you can > make it run fast. You might need to post a link to some details of this > summation method to get useful help. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Shuangxing Dai Eqation.pdf Description: Adobe PDF document ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How to add another electrostatic summation method in Gromacs
Hi, all, I was wondering how to add another electrostatic summation method--Wolf summation into Gromacs. Wolf summation is a treatment for summation of Coulombic energy. Since the formula of total potential energy for each ion is known, how to add this into Gromacs? According to Chapter 7, I should give the f(x) and f'(x). The formula of f and f' depends on the neighbours and varies from ion to ion, and I can not give f and f' without calculation. Since Wolf method uses the same error function as Ewald summation, it might be easier and possible to implement Wolf into Gromacs. If so, which files need to be modified? Hope I put my question clearly. Thank you in advance for suggestions and help. Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] combination rules -- the part aboutthecombinationrules
Thank you for your help. I checked all the force field, all of them are with default non-bond params in LJ. So I still need to try new solution. I add my non bond parameters in the .top file generated. Force field files were not changed. Then I use grompp, the error was: '[ nonbond_params ]' Invalid order for directive nonbond_params Rather confused by setting up Buckingham potential parameters... Thank you very much! 2009/2/26 Berk Hess > Hi, > > But do you need any other parameters than zinc and oxide? > If not, you can simply remove all other parameters. > If you need other atoms as well, you will need to find > a consistent force field, probably or completely LJ > or completely Buckingham. > > Berk > > > Date: Thu, 26 Feb 2009 09:22:26 +1100 > > From: mark.abra...@anu.edu.au > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] combination rules -- the part > aboutthecombinationrules > > > > Shuangxing Dai wrote: > > > Yes, "add parameters for crystalline zinc oxide, which require > > > Buckingham nonbonded interactions", that is what I am doing. I think I > > > have changed all the necessary parts for the Buckingham potential. Is > > > there any direct way to accomplish my goal? > > > > No, because it's not a reasonable goal. Your new atomtypes are talking a > > different vdW "language". That doesn't work. > > > > > Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type > > > > is 1. I only changed the parameters for Zn and O to Buckingham > > > parameters. And you said "add your functions in the right form in your > [ > > > molecule ] section" , I cannot find the right place to change. > > > > Chapter 5 of the manual. > > > > > And what > > > force field to choose if not ffgmx? > > > > That's your homework I'm afraid. You'll have to read the literature. > > > > Mark > > ___ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > -- > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] combination rules -- the part aboutthecombinationrules
Yes, "add parameters for crystalline zinc oxide, which require Buckingham nonbonded interactions", that is what I am doing. I think I have changed all the necessary parts for the Buckingham potential. Is there any direct way to accomplish my goal? Since in ffgmxnb.itp, all the nonbond_params are LJ if the default type is 1. I only changed the parameters for Zn and O to Buckingham parameters. And you said "add your functions in the right form in your [ molecule ] section" , I cannot find the right place to change. And what force field to choose if not ffgmx? Thank you very much. 2009/2/22 Mark Abraham > Shuangxing Dai wrote: > >> No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines >> of error informaion like this: >> ERROR 77 [file ffgmxnb.itp, line 144]: >> Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) >> > > Sure, this is predictable. This force field's files come filled with LJ > functions, and the default pertains to all of them. So you can either have > one form or the other. > > The issue is that if the force field generates the functions for > interactions based on the atom types, you can't mix the two types, since the > result is not defined. Sorry I didn't pick this up the first time, but if > you'd had a descriptive header "I'm trying to add parameters for (?) > crystalline zinc oxide, which require Buckingham nonbonded interactions" > then your strategy problem would have been obvious. > > I'm guessing here, but you may not be constrained by the default type if > you just add your functions in the right form in your [ molecule ] section. > This means you don't need to modify the force field files at all! However > you will need to supply a non-bonded interaction manually for any new atom > type with every atom type in your system. Those also seems likely to be > undefined. > > You also shouldn't be using ffgmx for a new simulation, because it has been > deprecated for years now. > > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] combination rules -- the part aboutthecombinationrules
No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines of error informaion like this: ERROR 77 [file ffgmxnb.itp, line 144]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 78 [file ffgmxnb.itp, line 145]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 79 [file ffgmxnb.itp, line 146]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 80 [file ffgmxnb.itp, line 147]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 81 [file ffgmxnb.itp, line 148]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 82 [file ffgmxnb.itp, line 149]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 83 [file ffgmxnb.itp, line 150]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 84 [file ffgmxnb.itp, line 151]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) ERROR 85 [file ffgmxnb.itp, line 152]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) - Original Message - From: Berk Hess To: Discussion list for GROMACS users Sent: Sunday, February 22, 2009 3:03 PM Subject: RE: [gmx-users] combination rules -- the part aboutthecombinationrules Hi, Is line 68 one of the lines you have added, or another one? Berk > From: shuangxing...@gmail.com > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] combination rules -- the part aboutthe combinationrules > Date: Sun, 22 Feb 2009 14:55:21 -0700 > > Thank you. I have referred to the manual and changed these parts as the > manual told me: > in ffgmx.itp: > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 2 1 no 1.0 1.0 > > in ffgmxnb.itp: > [ nonbond_params ] > ; i j func a b c6 > O O 2 92137.86 45.62876437 3090 > ZN O 2 51108.27 27.92516056 0 > ZN ZN 2 0 0.1 0 > But there is no change in the generated .top file. > When I use grompp, the errors are : > ERROR 1 [file ffgmxnb.itp, line 68]: > Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) > Maybe somewhere else need to be changed. Anyone knows why and how? > Thank you in advance. > > - Original Message - > From: "Mark Abraham" > To: "Discussion list for GROMACS users" > Sent: Friday, February 20, 2009 6:02 PM > Subject: Re: [gmx-users] combination rules -- the part aboutthe > combinationrules > > > > Shuangxing Dai wrote: > >> Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. > >> like > >> ; i j func a b c6 > >> Zn O 2 ... . But error occured.. > >> > >> ERROR 1 [file ffgmxnb.itp, line 270]: > >> > >> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) > >> > >> ERROR 2 [file ffgmxnb.itp, line 271]: > >> > >> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) > >> > >> ERROR 3 [file ffgmxnb.itp, line 272]: > >> > >> Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) > >> > >> I think I have indicated that the function type is 2 (means Buckingham). > >> Anything else need to do with this ? > > > > ... specify that the default nonbonded type is not LJ? Have a look in > > Chapter 5 of the manual. > > > >> Also, I want to fix some atoms in the boundary and specify displacement > >> to some atoms, anayone knows how to do this? > > > > You can freeze groups of atoms, or use position restraints, or pull groups > > of atoms, but you should look first in the manual for the information that > > is there. > > > > Mark > > ___ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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.
Re: [gmx-users] combination rules -- the part aboutthe combinationrules
Thank you. I have referred to the manual and changed these parts as the manual told me: in ffgmx.itp: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 in ffgmxnb.itp: [ nonbond_params ] ; ij func a b c6 OO292137.86 45.62876437 3090 ZNO251108.27 27.925160560 ZN ZN2 0 0.10 But there is no change in the generated .top file. When I use grompp, the errors are : ERROR 1 [file ffgmxnb.itp, line 68]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) Maybe somewhere else need to be changed. Anyone knows why and how? Thank you in advance. - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: Friday, February 20, 2009 6:02 PM Subject: Re: [gmx-users] combination rules -- the part aboutthe combinationrules Shuangxing Dai wrote: Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like ; ij func abc6 Zn O2 ... . But error occured.. ERROR 1 [file ffgmxnb.itp, line 270]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) ERROR 2 [file ffgmxnb.itp, line 271]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) ERROR 3 [file ffgmxnb.itp, line 272]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) I think I have indicated that the function type is 2 (means Buckingham). Anything else need to do with this ? ... specify that the default nonbonded type is not LJ? Have a look in Chapter 5 of the manual. Also, I want to fix some atoms in the boundary and specify displacement to some atoms, anayone knows how to do this? You can freeze groups of atoms, or use position restraints, or pull groups of atoms, but you should look first in the manual for the information that is there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] combination rules -- the part about the combinationrules
Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like ; ij func abc6 Zn O2 ... . But error occured.. ERROR 1 [file ffgmxnb.itp, line 270]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) ERROR 2 [file ffgmxnb.itp, line 271]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) ERROR 3 [file ffgmxnb.itp, line 272]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) I think I have indicated that the function type is 2 (means Buckingham). Anything else need to do with this ? Also, I want to fix some atoms in the boundary and specify displacement to some atoms, anayone knows how to do this? Thank you in advance. - Original Message - From: Berk Hess To: Discussion list for GROMACS users Sent: Wednesday, February 18, 2009 11:39 AM Subject: RE: [gmx-users] combination rules -- the part about the combinationrules Hi, No pairtypes are for bonded pair interactions, not for combinations of non-bonded interactions. The manual tells you how to do this: [ nonbond_params ] A_ii A_jj 2 a b c6 Berk > Date: Wed, 18 Feb 2009 13:31:43 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] combination rules -- the part about the combination rules > > For LJ interactions, use [ pairtypes ]. For Coulombics there is > unfortunately no analogous solution. I am not clear about exactly what > you want to do. What "parameters" are you interested in, or by this do > you just mean LJ and Q? > > Chris. > > -- original message -- > > Hello, > I was wondering how to set up parameters for interactions between > two different atoms A and B. Since for Gromacs parameters are defined > to each kind of atom, I cannot specify parameters between A and B. For > Buckingham potential, the rule was: > A_ij=(A_ii * A_jj)^(1/2) > So anyone know how to specify this value while not using the > combination rules? > --snip-- > > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Express yourself instantly with MSN Messenger! MSN Messenger -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] combination rules
Hello, I was wondering how to set up parameters for interactions between two different atoms A and B. Since for Gromacs parameters are defined to each kind of atom, I cannot specify parameters between A and B. For Buckingham potential, the rule was: A_ij=(A_ii * A_jj)^(1/2) So anyone know how to specify this value while not using the combination rules? I also have problem in installing xmgr. I use MacOSX 10.5.5. I type ./configure and got this error messege: ecme222-96-dhcp:xmgr-4.1.2 ssx$ ./configure creating cache ./config.cache checking host system type... configure: error: can not guess host type; you must specify one Anyone has encountered this before? Thank you. Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] new atom type and force field
Hi, all gmx users: I am doing a simulation with NaCl (and ZnO, GaN). I start with the .pdb file. But the Gromacs cannot recognize my new atom, such as Na, Cl. How to add new atoms to Gromacs? I am going to use periodical boundary conditions and LJ potential, shell model , apply loading , and check polarization. I do not know how to set the force field for LJ potential. Anyone know this can help me ? Thanks a lot! Shuangxing Dai___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
