Re: [gmx-users] pressure dependence on volume.
One less thing to worry about then. I will try to fix this in another way. Thanks. -- 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] pressure dependence on volume.
I believe you are too concentrated on writing questions, so that it does not leave you time to think about responses. Try to learn the manual a bit. Best luck. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sun, Oct 19, 2014 at 4:18 AM, Johnny Lu wrote: > I searched the energy file made by g_energy, and found that NPT frames with > very similar densities have very similar volume. > > So, I guess using density is same as using volume in this case. > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu wrote: > >> Would manually setting the box size make vacuum bubbles? >> >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu wrote: >> >>> my bad. that formula for density is wrong. But I till don't see why using >>> the same averaged density (instead of volume) for the NVT and NPT >>> simulations would give a different result. >>> >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu >>> wrote: >>> Was the density calculated by # particles / volume ? If so, using volume (as I did), and using density would give the same wrong pressure, upon transitioning from NPT to NVT. >>> >>> >> > -- > 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] pressure dependence on volume.
On Sun, Oct 19, 2014 at 4:18 PM, Johnny Lu wrote: > The averaged volume of the 1bar pressure NPT simulation over 150ns was very > clearly 298.5 nm^3. > But now, when I set the volume of the NVT simulation to 298.7 nm^3 by > starting from a NPT frame that has the volume, the average was 1.2 bar with > error estimate 0.53, over 52 ns. > ... so, indistiguishable from a wide range true values near 1 bar. No big surprise there. http://www.gromacs.org/Documentation/Terminology/Pressure The same tactic also didn't work for a 300 ns NPT simulation and > subsequently 300 ns NVT simulation. This NVT simulation pressure was > averaged to be around 4 bar. > > Why starting a NVT simulation from a NPT frame with the averaged NPT volume > didn't give the target pressure of 1 bar? Because that expectation is unreasonable for this system size over this time scale :-) Mark > On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar > wrote: > > > Hi Johnny, > > > > The density is M/V. The only parameter changing with pressure coupling is > > V, so the density and volume are fully correlated. No surprise there. > > > > Cheers, > > > > Tsjerk > > On Oct 19, 2014 2:27 AM, "Johnny Lu" wrote: > > > > > The frames with density closest to the average density also have > volumes > > > closest to the averaged volume. > > > > > > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu > > wrote: > > > > > > > I searched the energy file made by g_energy, and found that NPT > frames > > > > with very similar densities have very similar volume. > > > > > > > > So, I guess using density is same as using volume in this case. > > > > > > > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu > > > wrote: > > > > > > > >> Would manually setting the box size make vacuum bubbles? > > > >> > > > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu > > > >> wrote: > > > >> > > > >>> my bad. that formula for density is wrong. But I till don't see why > > > >>> using the same averaged density (instead of volume) for the NVT and > > NPT > > > >>> simulations would give a different result. > > > >>> > > > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu > > > > >>> wrote: > > > >>> > > > Was the density calculated by # particles / volume ? > > > > > > If so, using volume (as I did), and using density would give the > > same > > > wrong pressure, upon transitioning from NPT to NVT. > > > > > > >>> > > > >>> > > > >> > > > > > > > -- > > > 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. > -- 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] pressure dependence on volume.
I saved .cpt file every minute. And using the xvg file generated by g_energy, I picked the .cpt file with the volume that I want, and then run a NVT simulation, continuing from thee NPT .cpt file. The volume of the .cpt file of the NPT simulation should be same as the volume of the NVT file. Is it so? Or manually setting the volume makes some magical differences? On Sun, Oct 19, 2014 at 10:24 AM, Johnny Lu wrote: > Thanks for answering my questions too. > > On Sun, Oct 19, 2014 at 10:18 AM, Johnny Lu > wrote: > >> The averaged volume of the 1bar pressure NPT simulation over 150ns was >> very clearly 298.5 nm^3. >> But now, when I set the volume of the NVT simulation to 298.7 nm^3 by >> starting from a NPT frame that has the volume, the average was 1.2 bar with >> error estimate 0.53, over 52 ns. >> >> The same tactic also didn't work for a 300 ns NPT simulation and >> subsequently 300 ns NVT simulation. This NVT simulation pressure was >> averaged to be around 4 bar. >> >> Why starting a NVT simulation from a NPT frame with the averaged NPT >> volume didn't give the target pressure of 1 bar? >> >> >> >> On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar >> wrote: >> >>> Hi Johnny, >>> >>> The density is M/V. The only parameter changing with pressure coupling is >>> V, so the density and volume are fully correlated. No surprise there. >>> >>> Cheers, >>> >>> Tsjerk >>> On Oct 19, 2014 2:27 AM, "Johnny Lu" wrote: >>> >>> > The frames with density closest to the average density also have >>> volumes >>> > closest to the averaged volume. >>> > >>> > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu >>> wrote: >>> > >>> > > I searched the energy file made by g_energy, and found that NPT >>> frames >>> > > with very similar densities have very similar volume. >>> > > >>> > > So, I guess using density is same as using volume in this case. >>> > > >>> > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu >>> > wrote: >>> > > >>> > >> Would manually setting the box size make vacuum bubbles? >>> > >> >>> > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu >>> > >> wrote: >>> > >> >>> > >>> my bad. that formula for density is wrong. But I till don't see why >>> > >>> using the same averaged density (instead of volume) for the NVT >>> and NPT >>> > >>> simulations would give a different result. >>> > >>> >>> > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu >> > >>> > >>> wrote: >>> > >>> >>> > Was the density calculated by # particles / volume ? >>> > >>> > If so, using volume (as I did), and using density would give the >>> same >>> > wrong pressure, upon transitioning from NPT to NVT. >>> > >>> > >>> >>> > >>> >>> > >> >>> > > >>> > -- >>> > 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] pressure dependence on volume.
Thanks for answering my questions too. On Sun, Oct 19, 2014 at 10:18 AM, Johnny Lu wrote: > The averaged volume of the 1bar pressure NPT simulation over 150ns was > very clearly 298.5 nm^3. > But now, when I set the volume of the NVT simulation to 298.7 nm^3 by > starting from a NPT frame that has the volume, the average was 1.2 bar with > error estimate 0.53, over 52 ns. > > The same tactic also didn't work for a 300 ns NPT simulation and > subsequently 300 ns NVT simulation. This NVT simulation pressure was > averaged to be around 4 bar. > > Why starting a NVT simulation from a NPT frame with the averaged NPT > volume didn't give the target pressure of 1 bar? > > > > On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar > wrote: > >> Hi Johnny, >> >> The density is M/V. The only parameter changing with pressure coupling is >> V, so the density and volume are fully correlated. No surprise there. >> >> Cheers, >> >> Tsjerk >> On Oct 19, 2014 2:27 AM, "Johnny Lu" wrote: >> >> > The frames with density closest to the average density also have volumes >> > closest to the averaged volume. >> > >> > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu >> wrote: >> > >> > > I searched the energy file made by g_energy, and found that NPT frames >> > > with very similar densities have very similar volume. >> > > >> > > So, I guess using density is same as using volume in this case. >> > > >> > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu >> > wrote: >> > > >> > >> Would manually setting the box size make vacuum bubbles? >> > >> >> > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu >> > >> wrote: >> > >> >> > >>> my bad. that formula for density is wrong. But I till don't see why >> > >>> using the same averaged density (instead of volume) for the NVT and >> NPT >> > >>> simulations would give a different result. >> > >>> >> > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu >> > >>> wrote: >> > >>> >> > Was the density calculated by # particles / volume ? >> > >> > If so, using volume (as I did), and using density would give the >> same >> > wrong pressure, upon transitioning from NPT to NVT. >> > >> > >>> >> > >>> >> > >> >> > > >> > -- >> > 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] pressure dependence on volume.
The averaged volume of the 1bar pressure NPT simulation over 150ns was very clearly 298.5 nm^3. But now, when I set the volume of the NVT simulation to 298.7 nm^3 by starting from a NPT frame that has the volume, the average was 1.2 bar with error estimate 0.53, over 52 ns. The same tactic also didn't work for a 300 ns NPT simulation and subsequently 300 ns NVT simulation. This NVT simulation pressure was averaged to be around 4 bar. Why starting a NVT simulation from a NPT frame with the averaged NPT volume didn't give the target pressure of 1 bar? On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar wrote: > Hi Johnny, > > The density is M/V. The only parameter changing with pressure coupling is > V, so the density and volume are fully correlated. No surprise there. > > Cheers, > > Tsjerk > On Oct 19, 2014 2:27 AM, "Johnny Lu" wrote: > > > The frames with density closest to the average density also have volumes > > closest to the averaged volume. > > > > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu > wrote: > > > > > I searched the energy file made by g_energy, and found that NPT frames > > > with very similar densities have very similar volume. > > > > > > So, I guess using density is same as using volume in this case. > > > > > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu > > wrote: > > > > > >> Would manually setting the box size make vacuum bubbles? > > >> > > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu > > >> wrote: > > >> > > >>> my bad. that formula for density is wrong. But I till don't see why > > >>> using the same averaged density (instead of volume) for the NVT and > NPT > > >>> simulations would give a different result. > > >>> > > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu > > >>> wrote: > > >>> > > Was the density calculated by # particles / volume ? > > > > If so, using volume (as I did), and using density would give the > same > > wrong pressure, upon transitioning from NPT to NVT. > > > > >>> > > >>> > > >> > > > > > -- > > 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] pressure dependence on volume.
Hi Johnny, The density is M/V. The only parameter changing with pressure coupling is V, so the density and volume are fully correlated. No surprise there. Cheers, Tsjerk On Oct 19, 2014 2:27 AM, "Johnny Lu" wrote: > The frames with density closest to the average density also have volumes > closest to the averaged volume. > > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu wrote: > > > I searched the energy file made by g_energy, and found that NPT frames > > with very similar densities have very similar volume. > > > > So, I guess using density is same as using volume in this case. > > > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu > wrote: > > > >> Would manually setting the box size make vacuum bubbles? > >> > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu > >> wrote: > >> > >>> my bad. that formula for density is wrong. But I till don't see why > >>> using the same averaged density (instead of volume) for the NVT and NPT > >>> simulations would give a different result. > >>> > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu > >>> wrote: > >>> > Was the density calculated by # particles / volume ? > > If so, using volume (as I did), and using density would give the same > wrong pressure, upon transitioning from NPT to NVT. > > >>> > >>> > >> > > > -- > 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] pressure dependence on volume.
The frames with density closest to the average density also have volumes closest to the averaged volume. On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu wrote: > I searched the energy file made by g_energy, and found that NPT frames > with very similar densities have very similar volume. > > So, I guess using density is same as using volume in this case. > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu wrote: > >> Would manually setting the box size make vacuum bubbles? >> >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu >> wrote: >> >>> my bad. that formula for density is wrong. But I till don't see why >>> using the same averaged density (instead of volume) for the NVT and NPT >>> simulations would give a different result. >>> >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu >>> wrote: >>> Was the density calculated by # particles / volume ? If so, using volume (as I did), and using density would give the same wrong pressure, upon transitioning from NPT to NVT. >>> >>> >> > -- 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] pressure dependence on volume.
I searched the energy file made by g_energy, and found that NPT frames with very similar densities have very similar volume. So, I guess using density is same as using volume in this case. On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu wrote: > Would manually setting the box size make vacuum bubbles? > > On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu wrote: > >> my bad. that formula for density is wrong. But I till don't see why using >> the same averaged density (instead of volume) for the NVT and NPT >> simulations would give a different result. >> >> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu >> wrote: >> >>> Was the density calculated by # particles / volume ? >>> >>> If so, using volume (as I did), and using density would give the same >>> wrong pressure, upon transitioning from NPT to NVT. >>> >> >> > -- 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] pressure dependence on volume.
Would manually setting the box size make vacuum bubbles? On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu wrote: > my bad. that formula for density is wrong. But I till don't see why using > the same averaged density (instead of volume) for the NVT and NPT > simulations would give a different result. > > On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu wrote: > >> Was the density calculated by # particles / volume ? >> >> If so, using volume (as I did), and using density would give the same >> wrong pressure, upon transitioning from NPT to NVT. >> > > -- 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] pressure dependence on volume.
my bad. that formula for density is wrong. But I till don't see why using the same averaged density (instead of volume) for the NVT and NPT simulations would give a different result. On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu wrote: > Was the density calculated by # particles / volume ? > > If so, using volume (as I did), and using density would give the same > wrong pressure, upon transitioning from NPT to NVT. > -- 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] pressure dependence on volume.
Was the density calculated by # particles / volume ? If so, using volume (as I did), and using density would give the same wrong pressure, upon transitioning from NPT to NVT. -- 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] pressure dependence on volume.
Hey :) That is under the assumption that the pressure distribution is symmetric for a given density. That's rather unlikely, though. You should probably set the density to the average density for the pressure you want, so from the density distribution at 1 bar. Cheers, Tsjerk On Oct 18, 2014 9:06 AM, "Dr. Vitaly Chaban" wrote: > To achieve what you want you need to MANUALLY set the average DENSITY > which you obtained from NPT. That is, you MANUALLY adjust box side > length in the GRO file. > > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sat, Oct 18, 2014 at 1:47 AM, Johnny Lu wrote: > > I am trying to transit from NPT to NVT. > > Using the averaged volume of NPT for NVT somehow didn't give me the 1 bar > > pressure in NVT. > > I don't know why that happened. > > > > Was it the difference between constant pressure and constant volume heat > > capacity? But then, the thermostat should take care of that quite > quickly. > > After that, N, V, and T would be same for NPT simulation and the NVT > > simulation... which means the pressure should be the same. > > > > Both the NVT and NPT uses the V-rescale thermostat, and the NPT uses > > Berendsen barostat. > > > > Right now I'm selecting NPT frames with different volumes, and see if the > > NVT simulations continuing from those frames would give me the 1 bar > > pressure. > > > > On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul wrote: > > > >> > >> > >> On 10/17/14 11:49 AM, Johnny Lu wrote: > >> > >>> At least for real water, a 0.2% error in volume can mean the pressure > is > >>> ~30 bar when the target pressure is 1 bar. > >>> http://docs.engineeringtoolbox.com/documents/309/water-density- > >>> temperature-pressure_2.png > >>> > >>> On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu > >>> wrote: > >>> > >>> Hi. > > Mainly TIP3P water, 300K. The pressure is near 1 bar. > > A less than 1% error in volume would cause how much error in average > pressure? > > From three npt simulations of 72 ns with Berendsen barostat, I get > the > average volume is 298.5 nm^3. > > Continuing from a frame with volume very close to 298.5 nm^3 (~0.01 > deviation from this volume), I run NVT simulation that at first gives > a > system that doesn't seem to be at equilibrium. > > > >> Does that time point correspond to the desired pressure? The pressure > >> tensor is calculated from the virial and the kinetic energy, so those > are > >> the quantities you should be looking at for instantaneous pressures. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >> Department of Pharmaceutical Sciences > >> School of Pharmacy > >> Health Sciences Facility II, Room 629 > >> University of Maryland, Baltimore > >> 20 Penn St. > >> Baltimore, MD 21201 > >> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >> http://mackerell.umaryland.edu/~jalemkul > >> > >> == > >> -- > >> 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. > -- 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] pressure dependence on volume.
To achieve what you want you need to MANUALLY set the average DENSITY which you obtained from NPT. That is, you MANUALLY adjust box side length in the GRO file. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 18, 2014 at 1:47 AM, Johnny Lu wrote: > I am trying to transit from NPT to NVT. > Using the averaged volume of NPT for NVT somehow didn't give me the 1 bar > pressure in NVT. > I don't know why that happened. > > Was it the difference between constant pressure and constant volume heat > capacity? But then, the thermostat should take care of that quite quickly. > After that, N, V, and T would be same for NPT simulation and the NVT > simulation... which means the pressure should be the same. > > Both the NVT and NPT uses the V-rescale thermostat, and the NPT uses > Berendsen barostat. > > Right now I'm selecting NPT frames with different volumes, and see if the > NVT simulations continuing from those frames would give me the 1 bar > pressure. > > On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul wrote: > >> >> >> On 10/17/14 11:49 AM, Johnny Lu wrote: >> >>> At least for real water, a 0.2% error in volume can mean the pressure is >>> ~30 bar when the target pressure is 1 bar. >>> http://docs.engineeringtoolbox.com/documents/309/water-density- >>> temperature-pressure_2.png >>> >>> On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu >>> wrote: >>> >>> Hi. Mainly TIP3P water, 300K. The pressure is near 1 bar. A less than 1% error in volume would cause how much error in average pressure? From three npt simulations of 72 ns with Berendsen barostat, I get the average volume is 298.5 nm^3. Continuing from a frame with volume very close to 298.5 nm^3 (~0.01 deviation from this volume), I run NVT simulation that at first gives a system that doesn't seem to be at equilibrium. >> Does that time point correspond to the desired pressure? The pressure >> tensor is calculated from the virial and the kinetic energy, so those are >> the quantities you should be looking at for instantaneous pressures. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> 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] pressure dependence on volume.
I am trying to transit from NPT to NVT. Using the averaged volume of NPT for NVT somehow didn't give me the 1 bar pressure in NVT. I don't know why that happened. Was it the difference between constant pressure and constant volume heat capacity? But then, the thermostat should take care of that quite quickly. After that, N, V, and T would be same for NPT simulation and the NVT simulation... which means the pressure should be the same. Both the NVT and NPT uses the V-rescale thermostat, and the NPT uses Berendsen barostat. Right now I'm selecting NPT frames with different volumes, and see if the NVT simulations continuing from those frames would give me the 1 bar pressure. On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul wrote: > > > On 10/17/14 11:49 AM, Johnny Lu wrote: > >> At least for real water, a 0.2% error in volume can mean the pressure is >> ~30 bar when the target pressure is 1 bar. >> http://docs.engineeringtoolbox.com/documents/309/water-density- >> temperature-pressure_2.png >> >> On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu >> wrote: >> >> Hi. >>> >>> Mainly TIP3P water, 300K. The pressure is near 1 bar. >>> >>> A less than 1% error in volume would cause how much error in average >>> pressure? >>> >>> From three npt simulations of 72 ns with Berendsen barostat, I get the >>> average volume is 298.5 nm^3. >>> >>> Continuing from a frame with volume very close to 298.5 nm^3 (~0.01 >>> deviation from this volume), I run NVT simulation that at first gives a >>> system that doesn't seem to be at equilibrium. >>> >>> > Does that time point correspond to the desired pressure? The pressure > tensor is calculated from the virial and the kinetic energy, so those are > the quantities you should be looking at for instantaneous pressures. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] pressure dependence on volume.
On 10/17/14 11:49 AM, Johnny Lu wrote: At least for real water, a 0.2% error in volume can mean the pressure is ~30 bar when the target pressure is 1 bar. http://docs.engineeringtoolbox.com/documents/309/water-density-temperature-pressure_2.png On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu wrote: Hi. Mainly TIP3P water, 300K. The pressure is near 1 bar. A less than 1% error in volume would cause how much error in average pressure? From three npt simulations of 72 ns with Berendsen barostat, I get the average volume is 298.5 nm^3. Continuing from a frame with volume very close to 298.5 nm^3 (~0.01 deviation from this volume), I run NVT simulation that at first gives a system that doesn't seem to be at equilibrium. Does that time point correspond to the desired pressure? The pressure tensor is calculated from the virial and the kinetic energy, so those are the quantities you should be looking at for instantaneous pressures. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] pressure dependence on volume.
At least for real water, a 0.2% error in volume can mean the pressure is ~30 bar when the target pressure is 1 bar. http://docs.engineeringtoolbox.com/documents/309/water-density-temperature-pressure_2.png On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu wrote: > Hi. > > Mainly TIP3P water, 300K. The pressure is near 1 bar. > > A less than 1% error in volume would cause how much error in average > pressure? > > From three npt simulations of 72 ns with Berendsen barostat, I get the > average volume is 298.5 nm^3. > > Continuing from a frame with volume very close to 298.5 nm^3 (~0.01 > deviation from this volume), I run NVT simulation that at first gives a > system that doesn't seem to be at equilibrium. > > Thanks again. > -- 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] pressure dependence on volume.
Hi. Mainly TIP3P water, 300K. The pressure is near 1 bar. A less than 1% error in volume would cause how much error in average pressure? >From three npt simulations of 72 ns with Berendsen barostat, I get the average volume is 298.5 nm^3. Continuing from a frame with volume very close to 298.5 nm^3 (~0.01 deviation from this volume), I run NVT simulation that at first gives a system that doesn't seem to be at equilibrium. Thanks again. -- 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.
