Re: [gmx-users] density tip3p
Hi Nisha,I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each model of water has some deficiencies. I tried large number of cut-offs combinations LJ and QQ tyoes of interactions, but the density did not gange by more than 0.001g.cm-3. GreetingsZuzanaDňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS =integrator = sdtinit = 0dt = 0.002nsteps = 50nstcomm = 1nstxout = 0nstvout = 0nstfout = 0nstlog = 500nstenergy = 500nstxtcout = 0xtc-precision = 1000nstlist = 5ns_type = gridpbc = xyzrlist = 1.3coulombtype = pmercoulomb = 1.3epsilon-r = 1vdw-type = switchrvdw-switch = 1.0rvdw = 1.2DispCorr = EnerPresfourierspacing = 0.1fourier_nx = 0fourier_ny = 0fourier_nz = 0pme_order = 6ewald_rtol = 1e-06epsilon_surface = 0optimize_fft = notc_grps = systemtau_t = 0.1ref_t = 298Pcoupl = berendsentau_p = 1.0compressibility = 4.5e-05ref_p = 1.0constraints = all-bondsconstraint-algorithm = Lincsunconstrained-start = nolincs-order = 4lincs-warnangle = 30lincs-iter = 1gen_vel = yesgen_temp = 298.0gen_seed = 173529I also tried using mdp parameters as mentioned in some of the gromacs tutorials. I ran this simulation for 1ns and I am still getting density around 985g/l, which is low for tip3p water (27nm^3, 900 water molecules). I checked some of the publications and the values they obtained were ~998g/l. I checked for vacuum in my system, but I didn't see anything out of the ordinary. Any insights?ThanksNisha PQuoting nishap.pa...@utoronto.ca:Thanks. I will look up the manual again.Quoting Sander Pronk pr...@cbr.su.se:Hi Nisha,Looking at your .mdp, there are some issues that might lead to thebehavior that you describe:First: you should try to look up the published densities for tip3pwater at 300K - they might actually be close to what you get.Second: your neighbor list cut-off (rlist) might be too small tofully contain the charge groups (check the manual, section 7.3.11).Third: You haven't enabled long-range mean field correction for thepressure or energy. Expect the pressure to be strongly dependent oncut-off (see the same section).SanderOn Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:I have a box (3x3x3nm) of Tip3p water molecules ~900 and thedensity when I create the box using genbox is 997.177g/l. I didenergy minimization run and the potential energy did convergesmoothly, so I did NPT equilibration run of 100ps and I got thedensity value of 975g/l. Why does the density decrease after therun? these are the parameters that I used :RUN CONTROL PARAMETERSintegrator = mdtinit = 0dt = 0.002nsteps = 5nstcomm = 0nstxout = 0nstvout = 0nstfout = 0nstlog = 100nstenergy = 100nstxtcout = 0xtc_precision = 1000nstlist = 5ns-type = Gridpbc = xyzrlist = 1.1coulombtype = pmercoulomb = 1.1epsilon-r = 1vdw-type = switchrvdw-switch = 0.8rvdw = 1.0Tcoupl = V-rescaletc-grps = Systemtau_t = 0.1ref_t = 300Pcoupl = berendsentau_p = 0.5compressibility = 4e-05ref_p = 1.0constraints = all-bondsconstraint-algorithm = Lincsunconstrained-start = nolincs-order = 4lincs-iter = 1lincs-warnangle = 30Am I missing something?ThanksNisha Patel--gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use thewww interface or send it to
Re: [gmx-users] density tip3p
Hi Zuzana, You are right. I did get my density to ~0.986g/cm3, and I actually came across this other paper by Price and Brooks, and initially they get a density of Tip3p using pme at around 0.979g/cm3, but they tweak some of the parameters in oplsaa to get the correct density. I am not sure if you have tried that and if that helps at all, but also they are using a different simulation package. I am getting good rdf values for the water even with slightly low density, so I guess it is okay. Thanks Quoting Zuzana Benkova zuzana.benk...@savba.sk: Hi Nisha, I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each model of water has some deficiencies. I tried large number of cut-offs combinations LJ and QQ tyoes of interactions, but the density did not gange by more than 0.001g.cm-3. Greetings Zuzana Dňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS = integrator = sd tinit = 0 dt = 0.002 nsteps = 50 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 0 xtc-precision = 1000 nstlist = 5 ns_type = grid pbc = xyz rlist = 1.3 coulombtype = pme rcoulomb = 1.3 epsilon-r = 1 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.1 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tc_grps = system tau_t = 0.1 ref_t = 298 Pcoupl = berendsen tau_p = 1.0 compressibility = 4.5e-05 ref_p = 1.0 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 lincs-iter = 1 gen_vel = yes gen_temp = 298.0 gen_seed = 173529 I also tried using mdp parameters as mentioned in some of the gromacs tutorials. I ran this simulation for 1ns and I am still getting density around 985g/l, which is low for tip3p water (27nm^3, 900 water molecules). I checked some of the publications and the values they obtained were ~998g/l. I checked for vacuum in my system, but I didn't see anything out of the ordinary. Any insights? Thanks Nisha P Quoting nishap.pa...@utoronto.ca: Thanks. I will look up the manual again. Quoting Sander Pronk pr...@cbr.su.se: Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too small to fully contain the charge groups (check the manual, section 7.3.11). Third: You haven't enabled long-range mean field correction for the pressure or energy. Expect the pressure to be strongly dependent on cut-off (see the same section). Sander On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote: I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the density decrease after the run? these are the parameters that I used : RUN CONTROL PARAMETERS integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 0 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy = 100 nstxtcout = 0 xtc_precision = 1000 nstlist = 5 ns-type = Grid pbc = xyz rlist = 1.1 coulombtype = pme rcoulomb = 1.1 epsilon-r = 1 vdw-type = switch rvdw-switch = 0.8 rvdw = 1.0 Tcoupl = V-rescale tc-grps = System
Re: [gmx-users] density tip3p
Hi Nisha,I did not try OPLSAA since I need TIP3P model with CHARMM. With this FF hydrogens are also considered as interaction sites. This is not very good combination for GROMACS, but it appeared that the differences are not too big and the time required for simulation with H interacttion side is significantly larger. From my experience rdf is not too sensitive to cut-offs. Try to estimate for instance dielectric constant, dipole moment, diffusion coefficient to be entirely sure. But I think you are getting equlibrated system. Good luckZuzana Dňa 04/01/10, nishap.pa...@utoronto.ca napísal:Hi Zuzana, You are right. I did get my density to ~0.986g/cm3, and I actually came across this other paper by Price and Brooks, and initially they get a density of Tip3p using pme at around 0.979g/cm3, but they tweak some of the parameters in oplsaa to get the correct density. I am not sure if you have tried that and if that helps at all, but also they are using a different simulation package.I am getting good rdf values for the water even with slightly low density, so I guess it is okay.ThanksQuoting Zuzana Benkova zuzana.benk...@savba.sk:Hi Nisha,I have performed a benchmark simulations of TIP3P water and I stillobtained density 0.984g.cm-3. It looks that this model gives such adensity. If you look at JCP 79, 926, 1983 you will see that theauthors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsooother properties, each model of water has some deficiencies. I triedlarge number of cut-offs combinations LJ and QQ tyoes ofinteractions, but the density did not gange by more than 0.001g.cm-3.GreetingsZuzanaDňa 03/31/10, nishap.pa...@utoronto.ca napísal:Hello, So I looked at the manual and I changed my mdp parameters asfollows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS =integrator = sdtinit = 0dt = 0.002nsteps = 50nstcomm = 1nstxout = 0nstvout = 0nstfout = 0nstlog = 500nstenergy = 500nstxtcout = 0xtc-precision = 1000nstlist = 5ns_type = gridpbc = xyzrlist = 1.3coulombtype = pmercoulomb = 1.3epsilon-r = 1vdw-type = switchrvdw-switch = 1.0rvdw = 1.2DispCorr = EnerPresfourierspacing = 0.1fourier_nx = 0fourier_ny = 0fourier_nz = 0pme_order = 6ewald_rtol = 1e-06epsilon_surface = 0optimize_fft = notc_grps = systemtau_t = 0.1ref_t = 298Pcoupl = berendsentau_p = 1.0compressibility = 4.5e-05ref_p = 1.0constraints = all-bondsconstraint-algorithm = Lincsunconstrained-start = nolincs-order = 4lincs-warnangle = 30lincs-iter = 1gen_vel = yesgen_temp = 298.0gen_seed = 173529I also tried using mdp parameters as mentioned in some of the gromacstutorials. I ran this simulation for 1ns and I am still gettingdensity around 985g/l, which is low for tip3p water (27nm^3, 900water molecules). I checked some of the publications and the valuesthey obtained were ~998g/l. I checked for vacuum in my system, but Ididn't see anything out of the ordinary. Any insights?ThanksNisha PQuoting nishap.pa...@utoronto.ca:Thanks. I will look up the manual again.Quoting Sander Pronk pr...@cbr.su.se:Hi Nisha,Looking at your .mdp, there are some issues that might lead to thebehavior that you describe:First: you should try to look up the published densities for tip3pwater at 300K - they might actually be close to what you get.Second: your neighbor list cut-off (rlist) might be too small tofully contain the charge groups (check the manual, section 7.3.11).Third: You haven't enabled long-range mean field correction for thepressure or energy. Expect the pressure to be strongly dependent oncut-off (see the same section).SanderOn Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:I have a box (3x3x3nm) of Tip3p water molecules ~900 and thedensity when I create the box using genbox is 997.177g/l. I didenergy minimization run and the potential energy did convergesmoothly, so I did NPT equilibration run of 100ps and I got thedensity value of 975g/l. Why does the density decrease after therun? these are the parameters that I used :RUN CONTROL PARAMETERSintegrator = mdtinit = 0dt = 0.002nsteps = 5nstcomm = 0nstxout = 0nstvout = 0nstfout = 0nstlog = 100nstenergy =
Re: [gmx-users] density tip3p
Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS = integrator = sd tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy= 500 nstxtcout= 0 xtc-precision= 1000 nstlist = 5 ns_type = grid pbc = xyz rlist= 1.3 coulombtype = pme rcoulomb = 1.3 epsilon-r= 1 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.1 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tc_grps = system tau_t= 0.1 ref_t= 298 Pcoupl = berendsen tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 lincs-iter = 1 gen_vel = yes gen_temp = 298.0 gen_seed = 173529 I also tried using mdp parameters as mentioned in some of the gromacs tutorials. I ran this simulation for 1ns and I am still getting density around 985g/l, which is low for tip3p water (27nm^3, 900 water molecules). I checked some of the publications and the values they obtained were ~998g/l. I checked for vacuum in my system, but I didn't see anything out of the ordinary. Any insights? Thanks Nisha P Quoting nishap.pa...@utoronto.ca: Thanks. I will look up the manual again. Quoting Sander Pronk pr...@cbr.su.se: Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too small to fully contain the charge groups (check the manual, section 7.3.11). Third: You haven't enabled long-range mean field correction for the pressure or energy. Expect the pressure to be strongly dependent on cut-off (see the same section). Sander On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote: I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the density decrease after the run? these are the parameters that I used : RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 5 nstcomm = 0 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 0 xtc_precision= 1000 nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.1 coulombtype = pme rcoulomb = 1.1 epsilon-r= 1 vdw-type = switch rvdw-switch = 0.8 rvdw = 1.0 Tcoupl = V-rescale tc-grps = System tau_t= 0.1 ref_t= 300 Pcoupl = berendsen tau_p= 0.5 compressibility = 4e-05 ref_p= 1.0 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Am I missing something? Thanks Nisha Patel -- 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
Re: [gmx-users] density tip3p
On 1/04/2010 4:58 AM, nishap.pa...@utoronto.ca wrote: Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS = integrator = sd tinit = 0 dt = 0.002 nsteps = 50 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 0 xtc-precision = 1000 nstlist = 5 ns_type = grid pbc = xyz rlist = 1.3 coulombtype = pme rcoulomb = 1.3 epsilon-r = 1 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.1 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tc_grps = system tau_t = 0.1 ref_t = 298 Pcoupl = berendsen tau_p = 1.0 compressibility = 4.5e-05 ref_p = 1.0 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 lincs-iter = 1 gen_vel = yes gen_temp = 298.0 gen_seed = 173529 I also tried using mdp parameters as mentioned in some of the gromacs tutorials. I ran this simulation for 1ns and I am still getting density around 985g/l, which is low for tip3p water (27nm^3, 900 water molecules). I checked some of the publications and the values they obtained were ~998g/l. I checked for vacuum in my system, but I didn't see anything out of the ordinary. Any insights? Did they use stochastic dynamics? Have you equilibrated first before collecting your data? Mark Quoting nishap.pa...@utoronto.ca: Thanks. I will look up the manual again. Quoting Sander Pronk pr...@cbr.su.se: Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too small to fully contain the charge groups (check the manual, section 7.3.11). Third: You haven't enabled long-range mean field correction for the pressure or energy. Expect the pressure to be strongly dependent on cut-off (see the same section). Sander On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote: I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the density decrease after the run? these are the parameters that I used : RUN CONTROL PARAMETERS integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 0 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy = 100 nstxtcout = 0 xtc_precision = 1000 nstlist = 5 ns-type = Grid pbc = xyz rlist = 1.1 coulombtype = pme rcoulomb = 1.1 epsilon-r = 1 vdw-type = switch rvdw-switch = 0.8 rvdw = 1.0 Tcoupl = V-rescale tc-grps = System tau_t = 0.1 ref_t = 300 Pcoupl = berendsen tau_p = 0.5 compressibility = 4e-05 ref_p = 1.0 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Am I missing something? Thanks Nisha Patel -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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://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 Nisha Patel MSc Candidate Leslie Dan Faculty of Pharmacy Department of Pharmaceutical Sciences 144 College Street Room 1172 Toronto, ON M5S 3M2 Canada Telephone: 416-978-1536 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 Nisha Patel -- 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] density tip3p
Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too small to fully contain the charge groups (check the manual, section 7.3.11). Third: You haven't enabled long-range mean field correction for the pressure or energy. Expect the pressure to be strongly dependent on cut-off (see the same section). Sander On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote: I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the density decrease after the run? these are the parameters that I used : RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 5 nstcomm = 0 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 0 xtc_precision= 1000 nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.1 coulombtype = pme rcoulomb = 1.1 epsilon-r= 1 vdw-type = switch rvdw-switch = 0.8 rvdw = 1.0 Tcoupl = V-rescale tc-grps = System tau_t= 0.1 ref_t= 300 Pcoupl = berendsen tau_p= 0.5 compressibility = 4e-05 ref_p= 1.0 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Am I missing something? Thanks Nisha Patel -- 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] density tip3p
Thanks. I will look up the manual again. Quoting Sander Pronk pr...@cbr.su.se: Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too small to fully contain the charge groups (check the manual, section 7.3.11). Third: You haven't enabled long-range mean field correction for the pressure or energy. Expect the pressure to be strongly dependent on cut-off (see the same section). Sander On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote: I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the density decrease after the run? these are the parameters that I used : RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 5 nstcomm = 0 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 nstxtcout= 0 xtc_precision= 1000 nstlist = 5 ns-type = Grid pbc = xyz rlist= 1.1 coulombtype = pme rcoulomb = 1.1 epsilon-r= 1 vdw-type = switch rvdw-switch = 0.8 rvdw = 1.0 Tcoupl = V-rescale tc-grps = System tau_t= 0.1 ref_t= 300 Pcoupl = berendsen tau_p= 0.5 compressibility = 4e-05 ref_p= 1.0 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Am I missing something? Thanks Nisha Patel -- 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 Nisha Patel MSc Candidate Leslie Dan Faculty of Pharmacy Department of Pharmaceutical Sciences 144 College Street Room 1172 Toronto, ON M5S 3M2 Canada Telephone: 416-978-1536 -- 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
