Re: [gmx-users] Rigid water model
V-rescale as thermostat does give approximately the correct value for Cp. Thanks!! -- View this message in context: http://gromacs.5086.x6.nabble.com/Rigid-water-model-tp5015158p5015202.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Rigid water model
Setting the compressibility in gromacs actually is just as way adjust the stiffness of the barostat. Berendsen thermostat guarantees a Cp that is too low. Try v-rescale or nose-Hoover. See http://pubs.acs.org/doi/abs/10.1021/ct300688p For more info. Sent from my iPhone > On Mar 16, 2014, at 8:33, Mark Abraham wrote: > >> On Mar 14, 2014 11:06 PM, "Michelle Aranha" wrote: >> >> Hi! >> I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3 >> density, 10 ns NPT simulation (298 K & 1 bar)with Parinello Rahman > Barostat >> and Berendsen thermostat. > > Using a thermostat that produces the wrong velocity distribution is asking > for trouble. No idea if that's your main problem, though. > >> Here is my result for SPC water >> >> Kappa (J/m3)5.689E-10 >> Cp 22.8054 >> Cp- Cv 5.94102 >> >> The density, diffusion coefficient, the average configuration energy agree >> with previous results. However the heat capacity value is quite low as >> compared to 75 J/mol K of real water or even that has been previously > found >> with water models. I compared my values with a 2 ns and 10 ns simulations, >> but the heat capacity value shows no real improvement. I do not know much >> about quantum corrections hence I have not tried it. Will applying quantum >> corrections give the correct heat capacity? >> The isothermal compressibility reported by GROMACS is in J/m3 and the >> adiabatic bulk modulus is reported in m^3/J, could that be a mistake and >> should it be rather in (J/m^3)^-1 and J/m3 respectively. >> And, why does the isothermal compressibility change during the course of >> simulation if it has been fixed in the mdp file. > > A parameter for an algorithm and an observed property are two different > things! > > Mark > >> >> Best wishes, >> Michelle >> >> >> -- >> View this message in context: > http://gromacs.5086.x6.nabble.com/Rigid-water-model-tp5015158.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Rigid water model
On Mar 14, 2014 11:06 PM, "Michelle Aranha" wrote: > > Hi! > I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3 > density, 10 ns NPT simulation (298 K & 1 bar)with Parinello Rahman Barostat > and Berendsen thermostat. Using a thermostat that produces the wrong velocity distribution is asking for trouble. No idea if that's your main problem, though. > Here is my result for SPC water > > Kappa (J/m3)5.689E-10 > Cp 22.8054 > Cp- Cv 5.94102 > > The density, diffusion coefficient, the average configuration energy agree > with previous results. However the heat capacity value is quite low as > compared to 75 J/mol K of real water or even that has been previously found > with water models. I compared my values with a 2 ns and 10 ns simulations, > but the heat capacity value shows no real improvement. I do not know much > about quantum corrections hence I have not tried it. Will applying quantum > corrections give the correct heat capacity? > The isothermal compressibility reported by GROMACS is in J/m3 and the > adiabatic bulk modulus is reported in m^3/J, could that be a mistake and > should it be rather in (J/m^3)^-1 and J/m3 respectively. > And, why does the isothermal compressibility change during the course of > simulation if it has been fixed in the mdp file. A parameter for an algorithm and an observed property are two different things! Mark > > Best wishes, > Michelle > > > -- > View this message in context: http://gromacs.5086.x6.nabble.com/Rigid-water-model-tp5015158.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Rigid water model
Hi! I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3 density, 10 ns NPT simulation (298 K & 1 bar)with Parinello Rahman Barostat and Berendsen thermostat. Here is my result for SPC water Kappa (J/m3)5.689E-10 Cp 22.8054 Cp- Cv 5.94102 The density, diffusion coefficient, the average configuration energy agree with previous results. However the heat capacity value is quite low as compared to 75 J/mol K of real water or even that has been previously found with water models. I compared my values with a 2 ns and 10 ns simulations, but the heat capacity value shows no real improvement. I do not know much about quantum corrections hence I have not tried it. Will applying quantum corrections give the correct heat capacity? The isothermal compressibility reported by GROMACS is in J/m3 and the adiabatic bulk modulus is reported in m^3/J, could that be a mistake and should it be rather in (J/m^3)^-1 and J/m3 respectively. And, why does the isothermal compressibility change during the course of simulation if it has been fixed in the mdp file. Best wishes, Michelle -- View this message in context: http://gromacs.5086.x6.nabble.com/Rigid-water-model-tp5015158.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
