Re: [gmx-users] Non-equilibrium Viscosity Calculation
Hi, David; Thank you so much for your prompt response. Your answer is really helpful. On Mon, Apr 20, 2009 at 10:31 PM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Hi, David: >> >> I performed the NEMD and got the following results for averaging the >> last 1 ns. So the second column should be the acceleration and last >> column should be the 1/viscosity. But notice that there are so many >> big negative numbers, which makes the average negative. Can you help >> me out here? what would be possible reason for this. > > xmgrace will tell you which is which, I think the first is shear viscosity > and the second bulk viscosity. Your system might be too smal (Berk Hess > recommends at least 1000 molecules) or the simulation too short. However > bulk viscosity is much more difficult to get right. > Once more, read the literature, and use the tools (xmgrace) the information > is in the xvg file, but you cut it out here. >> >> 1000.61 -0.007012 -369.713501 >> 1020.61 0.006066 320.372314 >> 1040.00 0.002330 122.940369 >> 1060.00 -0.001427 -75.253372 >> 1080.00 0.002888 152.323944 >> 1100.00 0.005696 300.385651 >> 1120.00 0.002224 117.322388 >> 1140.00 0.005990 316.127655 >> 1160.00 0.008966 472.723846 >> 1180.00 0.004485 236.538010 >> 1200.00 -0.000249 -13.136140 >> 1220.00 0.005020 264.962219 >> 1240.00 0.009248 488.308197 >> 1260.00 -0.000559 -29.509850 >> 1280.00 -0.003190 -168.296112 >> 1300.000122 0.002394 126.418747 >> 1320.000122 0.003682 194.374222 >> 1340.000122 0.000371 19.600368 >> 1360.000122 -0.002311 -122.002975 >> 1380.000122 0.001776 93.685326 >> 1400.000122 -0.003357 -177.067062 >> 1420.000122 -0.002963 -156.359772 >> 1440.000122 -0.001078 -56.895496 >> 1460.000122 -0.002273 -119.947853 >> 1480.000122 -0.000658 -34.716648 >> 1500.000122 -0.000928 -48.969398 >> 1520.000122 0.003464 182.804337 >> 1540.000122 -0.001149 -60.652023 >> 1560.000122 0.004629 244.299088 >> 1580.000122 0.000485 25.557356 >> 1600.000122 0.002339 123.374527 >> 1620.000122 0.002612 137.982239 >> 1640.000122 0.002827 149.150589 >> 1660.000122 -0.001614 -85.147079 >> 1680.000122 0.005144 271.660522 >> 1700.000122 -0.002053 -108.302643 >> 1720.000122 0.006096 321.414948 >> 1740.000122 0.006021 317.682129 >> 1760.000122 -0.001203 -63.409481 >> 1780.000122 0.000394 20.755482 >> 1800.000122 0.001910 100.748962 >> 1820.000122 -0.001588 -83.742523 >> 1840.000122 0.002268 119.578842 >> 1860.000122 0.002422 127.769302 >> 1880.000122 -0.000288 -15.188296 >> 1900.000122 0.003324 175.257568 >> 1920.000122 0.003688 194.440231 >> 1940.000122 0.005800 305.705505 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel >> wrote: >>> >>> Yanmei Song wrote: Yes, I want to get the equilibrium viscosity. My question is how I can identify the system approach a zero acceleration after I try several values. Thank you so much for your help. >>> >>> Plot viscosity as a function of acceleration. Check the reference >>> (Wensink >>> et al.) that I mailed earlier. On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel wrote: > > Yanmei Song wrote: >> >> Dear David: >> >> Thank you for your answer. i still have several questions. >> >> Do I have to start the non-equilibrium simulation after the system >> reach the equilibrium? Or I just need to start at the same starting >> point as the my equilibrium systems? > > At least equilibrium density. >> >> What I need to do is just add the cos_acceleration: to the mdp file >> and nothing else need to be changed, right? Also what do you mean by >> "You need to do a few values such that you can extrapolate to zero >> acceleration." > > You are interested (I assume) in the equilibrium viscosity, therefore > you > need to do this extrapolation. You can not assume that a small > acceleration > is small enough. >> >> After I finish the run, what option I should use for g_energy in order >> to get the viscosity? > > No option. > > Just do it (tm). >> >> Thank you so much in advance! >> >> On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel >> wrote: >>> >>> Yanmei Song wrote: Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options,
Re: [gmx-users] Non-equilibrium Viscosity Calculation
Yanmei Song wrote: Hi, David: I performed the NEMD and got the following results for averaging the last 1 ns. So the second column should be the acceleration and last column should be the 1/viscosity. But notice that there are so many big negative numbers, which makes the average negative. Can you help me out here? what would be possible reason for this. xmgrace will tell you which is which, I think the first is shear viscosity and the second bulk viscosity. Your system might be too smal (Berk Hess recommends at least 1000 molecules) or the simulation too short. However bulk viscosity is much more difficult to get right. Once more, read the literature, and use the tools (xmgrace) the information is in the xvg file, but you cut it out here. 1000.61 -0.007012 -369.713501 1020.610.006066 320.372314 1040.000.002330 122.940369 1060.00 -0.001427 -75.253372 1080.000.002888 152.323944 1100.000.005696 300.385651 1120.000.002224 117.322388 1140.000.005990 316.127655 1160.000.008966 472.723846 1180.000.004485 236.538010 1200.00 -0.000249 -13.136140 1220.000.005020 264.962219 1240.000.009248 488.308197 1260.00 -0.000559 -29.509850 1280.00 -0.003190 -168.296112 1300.0001220.002394 126.418747 1320.0001220.003682 194.374222 1340.0001220.000371 19.600368 1360.000122 -0.002311 -122.002975 1380.0001220.001776 93.685326 1400.000122 -0.003357 -177.067062 1420.000122 -0.002963 -156.359772 1440.000122 -0.001078 -56.895496 1460.000122 -0.002273 -119.947853 1480.000122 -0.000658 -34.716648 1500.000122 -0.000928 -48.969398 1520.0001220.003464 182.804337 1540.000122 -0.001149 -60.652023 1560.0001220.004629 244.299088 1580.0001220.000485 25.557356 1600.0001220.002339 123.374527 1620.0001220.002612 137.982239 1640.0001220.002827 149.150589 1660.000122 -0.001614 -85.147079 1680.0001220.005144 271.660522 1700.000122 -0.002053 -108.302643 1720.0001220.006096 321.414948 1740.0001220.006021 317.682129 1760.000122 -0.001203 -63.409481 1780.0001220.000394 20.755482 1800.0001220.001910 100.748962 1820.000122 -0.001588 -83.742523 1840.0001220.002268 119.578842 1860.0001220.002422 127.769302 1880.000122 -0.000288 -15.188296 1900.0001220.003324 175.257568 1920.0001220.003688 194.440231 1940.0001220.005800 305.705505 On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel wrote: Yanmei Song wrote: Yes, I want to get the equilibrium viscosity. My question is how I can identify the system approach a zero acceleration after I try several values. Thank you so much for your help. Plot viscosity as a function of acceleration. Check the reference (Wensink et al.) that I mailed earlier. On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel wrote: Yanmei Song wrote: Dear David: Thank you for your answer. i still have several questions. Do I have to start the non-equilibrium simulation after the system reach the equilibrium? Or I just need to start at the same starting point as the my equilibrium systems? At least equilibrium density. What I need to do is just add the cos_acceleration: to the mdp file and nothing else need to be changed, right? Also what do you mean by "You need to do a few values such that you can extrapolate to zero acceleration." You are interested (I assume) in the equilibrium viscosity, therefore you need to do this extrapolation. You can not assume that a small acceleration is small enough. After I finish the run, what option I should use for g_energy in order to get the viscosity? No option. Just do it (tm). Thank you so much in advance! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel wrote: Yanmei Song wrote: Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options, right? acc_grps: accelerate: cos_acceleration: Just the last one. My question is: first, how to set the value of cos_acceleration: ? You need to do a few values such that you can extrapolate to zero acceleration. Second, after I finish the run, how can I get the viscosity from the simulation result? Anyone has done this yet? Thank you so much for your answer in advance. g_energy. J Chem Phys 116 (2002) 209-217 J Chem Phys 119 (2003) 7308-7317 -- 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.sesp...@gromacs.org http:
[gmx-users] How to understand the pull geometry of cylinder
Hi everyone, My colleague and I can not understand the picture of parameter of pull geometry of cylinder. How to determine the reference COM? How does the pulled group move? It is apprecited if someone gives me a simple picture of the parameter. A sketch map is OK. Thanks in advance. - pull geometry cylinder Designed for pulling with respect to a layer where the reference COM is given by a local cylindrical part of the reference group. The pulling is in the direction of pull vec,which should have only a z-component. >From the reference group a cylinder is selected for determining the COM, with the axis given by the x/y location of the group to be pulled and two radii. The radius pull r1 gives the radius within which all the relative weights are one, between pull r1 and pull r0 the weights are switched to zero. Mass weighting is also used. -- wende ___ 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] Non-equilibrium Viscosity Calculation
Hi, David: I performed the NEMD and got the following results for averaging the last 1 ns. So the second column should be the acceleration and last column should be the 1/viscosity. But notice that there are so many big negative numbers, which makes the average negative. Can you help me out here? what would be possible reason for this. 1000.61 -0.007012 -369.713501 1020.610.006066 320.372314 1040.000.002330 122.940369 1060.00 -0.001427 -75.253372 1080.000.002888 152.323944 1100.000.005696 300.385651 1120.000.002224 117.322388 1140.000.005990 316.127655 1160.000.008966 472.723846 1180.000.004485 236.538010 1200.00 -0.000249 -13.136140 1220.000.005020 264.962219 1240.000.009248 488.308197 1260.00 -0.000559 -29.509850 1280.00 -0.003190 -168.296112 1300.0001220.002394 126.418747 1320.0001220.003682 194.374222 1340.0001220.000371 19.600368 1360.000122 -0.002311 -122.002975 1380.0001220.001776 93.685326 1400.000122 -0.003357 -177.067062 1420.000122 -0.002963 -156.359772 1440.000122 -0.001078 -56.895496 1460.000122 -0.002273 -119.947853 1480.000122 -0.000658 -34.716648 1500.000122 -0.000928 -48.969398 1520.0001220.003464 182.804337 1540.000122 -0.001149 -60.652023 1560.0001220.004629 244.299088 1580.0001220.000485 25.557356 1600.0001220.002339 123.374527 1620.0001220.002612 137.982239 1640.0001220.002827 149.150589 1660.000122 -0.001614 -85.147079 1680.0001220.005144 271.660522 1700.000122 -0.002053 -108.302643 1720.0001220.006096 321.414948 1740.0001220.006021 317.682129 1760.000122 -0.001203 -63.409481 1780.0001220.000394 20.755482 1800.0001220.001910 100.748962 1820.000122 -0.001588 -83.742523 1840.0001220.002268 119.578842 1860.0001220.002422 127.769302 1880.000122 -0.000288 -15.188296 1900.0001220.003324 175.257568 1920.0001220.003688 194.440231 1940.0001220.005800 305.705505 On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Yes, I want to get the equilibrium viscosity. My question is how I can >> identify the system approach a zero acceleration after I try several >> values. Thank you so much for your help. > > Plot viscosity as a function of acceleration. Check the reference (Wensink > et al.) that I mailed earlier. >> >> On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel >> wrote: >>> >>> Yanmei Song wrote: Dear David: Thank you for your answer. i still have several questions. Do I have to start the non-equilibrium simulation after the system reach the equilibrium? Or I just need to start at the same starting point as the my equilibrium systems? >>> >>> At least equilibrium density. What I need to do is just add the cos_acceleration: to the mdp file and nothing else need to be changed, right? Also what do you mean by "You need to do a few values such that you can extrapolate to zero acceleration." >>> >>> You are interested (I assume) in the equilibrium viscosity, therefore you >>> need to do this extrapolation. You can not assume that a small >>> acceleration >>> is small enough. After I finish the run, what option I should use for g_energy in order to get the viscosity? >>> >>> No option. >>> >>> Just do it (tm). Thank you so much in advance! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel wrote: > > Yanmei Song wrote: >> >> Dear All: >> >> I wanted to get the viscosity of my simulated polymer system. From the >> manual it said that : GROMACS also has a non-equilibrium method for >> determining the viscosity" (page 123) Does this mean I just need to do >> a separate non-equilibrium MD run? In terms of mdp file, I just need >> to add the following options, right? >> acc_grps: >> accelerate: >> cos_acceleration: > > Just the last one. > >> My question is: first, how to set the value of cos_acceleration: ? > > You need to do a few values such that you can extrapolate to zero > acceleration. > >> Second, after I finish the run, how can I get the viscosity from the >> simulation result? Anyone has done this yet? Thank you so much for >> your answer in advance. >> > g_energy. > > J Chem Phys 116 (2002) 209-217 > J Chem Phys 119 (2003) 7308-7317 > -- > 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 > ___
Re: [gmx-users] Non-equilibrium Viscosity Calculation
Yanmei Song wrote: Yes, I want to get the equilibrium viscosity. My question is how I can identify the system approach a zero acceleration after I try several values. Thank you so much for your help. Plot viscosity as a function of acceleration. Check the reference (Wensink et al.) that I mailed earlier. On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel wrote: Yanmei Song wrote: Dear David: Thank you for your answer. i still have several questions. Do I have to start the non-equilibrium simulation after the system reach the equilibrium? Or I just need to start at the same starting point as the my equilibrium systems? At least equilibrium density. What I need to do is just add the cos_acceleration: to the mdp file and nothing else need to be changed, right? Also what do you mean by "You need to do a few values such that you can extrapolate to zero acceleration." You are interested (I assume) in the equilibrium viscosity, therefore you need to do this extrapolation. You can not assume that a small acceleration is small enough. After I finish the run, what option I should use for g_energy in order to get the viscosity? No option. Just do it (tm). Thank you so much in advance! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel wrote: Yanmei Song wrote: Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options, right? acc_grps: accelerate: cos_acceleration: Just the last one. My question is: first, how to set the value of cos_acceleration: ? You need to do a few values such that you can extrapolate to zero acceleration. Second, after I finish the run, how can I get the viscosity from the simulation result? Anyone has done this yet? Thank you so much for your answer in advance. g_energy. J Chem Phys 116 (2002) 209-217 J Chem Phys 119 (2003) 7308-7317 -- 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.sesp...@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 -- 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.sesp...@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 -- 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.sesp...@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
Re: [gmx-users] Non-equilibrium Viscosity Calculation
Yes, I want to get the equilibrium viscosity. My question is how I can identify the system approach a zero acceleration after I try several values. Thank you so much for your help. On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Dear David: >> >> Thank you for your answer. i still have several questions. >> >> Do I have to start the non-equilibrium simulation after the system >> reach the equilibrium? Or I just need to start at the same starting >> point as the my equilibrium systems? > > At least equilibrium density. >> >> What I need to do is just add the cos_acceleration: to the mdp file >> and nothing else need to be changed, right? Also what do you mean by >> "You need to do a few values such that you can extrapolate to zero >> acceleration." > > You are interested (I assume) in the equilibrium viscosity, therefore you > need to do this extrapolation. You can not assume that a small acceleration > is small enough. >> >> After I finish the run, what option I should use for g_energy in order >> to get the viscosity? > > No option. > > Just do it (tm). >> >> Thank you so much in advance! >> >> On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel >> wrote: >>> >>> Yanmei Song wrote: Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options, right? acc_grps: accelerate: cos_acceleration: >>> >>> Just the last one. >>> My question is: first, how to set the value of cos_acceleration: ? >>> >>> You need to do a few values such that you can extrapolate to zero >>> acceleration. >>> Second, after I finish the run, how can I get the viscosity from the simulation result? Anyone has done this yet? Thank you so much for your answer in advance. >>> g_energy. >>> >>> J Chem Phys 116 (2002) 209-217 >>> J Chem Phys 119 (2003) 7308-7317 >>> >>> -- >>> 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 list gmx-us...@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 list gmx-us...@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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] Non-equilibrium Viscosity Calculation
Yanmei Song wrote: Dear David: Thank you for your answer. i still have several questions. Do I have to start the non-equilibrium simulation after the system reach the equilibrium? Or I just need to start at the same starting point as the my equilibrium systems? At least equilibrium density. What I need to do is just add the cos_acceleration: to the mdp file and nothing else need to be changed, right? Also what do you mean by "You need to do a few values such that you can extrapolate to zero acceleration." You are interested (I assume) in the equilibrium viscosity, therefore you need to do this extrapolation. You can not assume that a small acceleration is small enough. After I finish the run, what option I should use for g_energy in order to get the viscosity? No option. Just do it (tm). Thank you so much in advance! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel wrote: Yanmei Song wrote: Dear All: I wanted to get the viscosity of my simulated polymer system. From the manual it said that : GROMACS also has a non-equilibrium method for determining the viscosity" (page 123) Does this mean I just need to do a separate non-equilibrium MD run? In terms of mdp file, I just need to add the following options, right? acc_grps: accelerate: cos_acceleration: Just the last one. My question is: first, how to set the value of cos_acceleration: ? You need to do a few values such that you can extrapolate to zero acceleration. Second, after I finish the run, how can I get the viscosity from the simulation result? Anyone has done this yet? Thank you so much for your answer in advance. g_energy. J Chem Phys 116 (2002) 209-217 J Chem Phys 119 (2003) 7308-7317 -- 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.sesp...@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 -- 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.sesp...@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
Re: [gmx-users] Non-equilibrium Viscosity Calculation
Dear David: Thank you for your answer. i still have several questions. Do I have to start the non-equilibrium simulation after the system reach the equilibrium? Or I just need to start at the same starting point as the my equilibrium systems? What I need to do is just add the cos_acceleration: to the mdp file and nothing else need to be changed, right? Also what do you mean by "You need to do a few values such that you can extrapolate to zero acceleration." After I finish the run, what option I should use for g_energy in order to get the viscosity? Thank you so much in advance! On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel wrote: > Yanmei Song wrote: >> >> Dear All: >> >> I wanted to get the viscosity of my simulated polymer system. From the >> manual it said that : GROMACS also has a non-equilibrium method for >> determining the viscosity" (page 123) Does this mean I just need to do >> a separate non-equilibrium MD run? In terms of mdp file, I just need >> to add the following options, right? >> acc_grps: >> accelerate: >> cos_acceleration: > > Just the last one. > >> >> My question is: first, how to set the value of cos_acceleration: ? > > You need to do a few values such that you can extrapolate to zero > acceleration. > >> Second, after I finish the run, how can I get the viscosity from the >> simulation result? Anyone has done this yet? Thank you so much for >> your answer in advance. >> > g_energy. > > J Chem Phys 116 (2002) 209-217 > J Chem Phys 119 (2003) 7308-7317 >> >> > > > -- > 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 list gmx-us...@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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] g_msd
I had the same problem before. I think the best way to do it is to analyze every group separately. On Mon, Apr 20, 2009 at 1:53 AM, Borys Szefczyk wrote: > Dear Gromacs users, > > I'm doing some tests on molten sodium chloride, trying to calculate > self-diffusion coefficients of both ions. Could someone tell me what > actually does the -ngroup switch of the g_msd program? > > When I compute D for chlorine only, I get 6.4607e-5 cm^2/s; > for sodium only, I get D = 9.0996e-5 cm^2/s. > > But when I set -ngroup to 2 and specify both groups (NA and CL) > subsequently, I get: > D[ NA+] = 9.0976e-5 cm^2/s > D[ CL-] = 0.9128e-5 cm^2/s > Plot of MSD looks fine for NA, but not for CL - it's a saw-shaped, > almost flat line. > > If I enter the groups in reverse order, first CL, then NA, I get: > D[ CL-] = 6.4607e-5 cm^2/s > D[ NA+] = 4.2326e-5 cm^2/s > Again, first plot look fine, the second - not. > > Why these results differ? > > Regards, > Borys Szefczyk > > > -- > REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, > Department of Chemistry, & Institute of Physical & Theoretical Chemistry, > Faculty of Science, & Wroclaw University of Technology > University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk > ___ > gmx-users mailing list gmx-us...@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 > -- Yanmei Song Department of Chemical Engineering ASU ___ 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] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Hi, Thanks for answering and sorry to take so long to reply. After your response I went seach for more information about that. What I read here in the list is that some people uses antechamber to generate am1-bcc charges (or RESP charges using Gaussian program) and convert the output files to a .top file (using the amb2gmx.pl script) that can be used in gromacs, however, nobody says the kind of ff they intend to use that charges with. Do these type of charges can also be used with Gromos96 ff ( 43a1)? Thanks in advance! You could also use R.E.D.-III.2 http://q4md-forcefieldtools.org/RED/ to generate RESP and ESP charges directly embedded in force field libraries (Tripos mol2 file format). You can select various algorithm to compute the MEP (CHELPG, or Connolly surface) and various fitting approaches (RESP or ESP). R.E.D. Server which interfaces R.E.D.-IV is now available http://q4md-forcefieldtools.org/REDS/ as well. - You could use R.E.D. to generate Tripos mol2 files. - Then, create the corresponding prmtop file using LEaP. - Finally, convert the prmtop file into a format recognized by Gromacs. regards, Francois ___ 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] g_msd
Dear Gromacs users, I'm doing some tests on molten sodium chloride, trying to calculate self-diffusion coefficients of both ions. Could someone tell me what actually does the -ngroup switch of the g_msd program? When I compute D for chlorine only, I get 6.4607e-5 cm^2/s; for sodium only, I get D = 9.0996e-5 cm^2/s. But when I set -ngroup to 2 and specify both groups (NA and CL) subsequently, I get: D[ NA+] = 9.0976e-5 cm^2/s D[ CL-] = 0.9128e-5 cm^2/s Plot of MSD looks fine for NA, but not for CL - it's a saw-shaped, almost flat line. If I enter the groups in reverse order, first CL, then NA, I get: D[ CL-] = 6.4607e-5 cm^2/s D[ NA+] = 4.2326e-5 cm^2/s Again, first plot look fine, the second - not. Why these results differ? Regards, Borys Szefczyk -- REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, Department of Chemistry, & Institute of Physical & Theoretical Chemistry, Faculty of Science, & Wroclaw University of Technology University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk ___ 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] Probably a bug in nstenergy?
Lee Soin wrote: I'm using version 4.0.4. Here's my .mdp file: OK, so make two directories for versions of the .mdp file with different nstenergy, run grompp on each to create two .tpr files, and run both of those. You should see corresponding different rates of energy file output. As DvdS suggested, you may have omitted to re-run grompp, or used the wrong .mdp file or wrong .tpr file or looked at the wrong results. 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
Re: [gmx-users] Probably a bug in nstenergy?
I'm using version 4.0.4. Here's my .mdp file: ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1000 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld_seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells niter= 100 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 0 ; Output frequency and precision for xtc file nstxtcout= 1 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; 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_switch = 0 rcoulomb = 1. ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; 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= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc_grps = Protein Other ; Time constant (ps) and reference temperature (K) tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Scaling of reference coordinates, No, All or C
