Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Thanks for the detailed reply. This is a really good example for the manifold of traps you can tap into when treating long range forces. Flo * Mark Abraham mark.abra...@anu.edu.au [2009-06-20 14:55:39 +1000]: Florian Dommert wrote: * Mark Abraham mark.abra...@anu.edu.au [2009-06-20 11:54:46 +1000]: When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity != 1. With the mentionend Ewald methods I should be able to reproduce exactly the same circumstances like in a reaction-field setup. So at the moment I can imagine just one critical point, when using SPME/PME/PPPM or an Ewald sum is the big set of parameters that have to adapted in order to obtain an appropriate accuracy of the forces. In the reaction field method you just have two parameters: the cutoff and epsilon_r. The other algorithms require addtionally require the input of an appropriate size for used grid in Fourier space and in case of SPME/PME/PPPM also an interpolation order. Finally you need to set the splitting paramter correctly, otherwise you will obtain unaccurate forces. So there can be a very large error introduced, when applying the wrong parameters to the Ewald methods. The heat up of the water is also just related to extremly inaccurate electrostatic forces, since with PBC an infinite system is simulated and just a very small amount of the electrostatic interaction that is of long range nature is calculated. Therefore an large error is not unexpected. Finally the only restriction of Ewald I see is the requirement of PBC, where I can reach any level of accuracy for the electrostatic force given by certain charge distribution, don't I ? I really haven't understood you, sorry. I think that I a complete wrong idea of an simulation using a Reaction field, so I have to get a correct picture. Because when investigating a protein you require a physiological environment with corresponding ions to provide a certain pH value. Is this finally all contained in the force field parameters ? In principle, yes, however not even in theory is this true for the commonly-used force fields. Typically they were parameterized to reproduce a range of experimental or quantum-chemical data, but the scale of this parameterization problem was large enough that considering solvents of non-pure water would have been too much (even if data was available). One might demonstrate post-factum that a force field does a reasonable job in such a case. One might also demonstrate that a force field does a reasonable job under a different electrostatic treatment. This would make things clear and enlight my foggy insight in this special way to treat electrostatic forces. Furthermore I assume no periodic boundary conditions are used then ? One's electrostatic model need not be confounded with the boundary conditions of the simulation. For Ewald-family methods, PBC is required, introducing the potential for periodicity artefacts. For other methods (cut-off, fast multipole and variants) one has the option of choosing a different boundary condition (e.g. non-periodic (RF) vacuum containing a restrained spherical shell of water around free water, or a large protein complex in vacuo) and suffering artefects from those boundary conditions, rather than perhaps periodicity-induced ones. In particular for RF, the assumption of homogeneity would suggest not using PBC. With enough solvent, in practice that assumption would be approximately true even under PBC. You just simulate a protein/polymer/molecule and assume that it is surrounded by a medium with a certain epsilon_r. Sure, but the RF model as applied to each particle does not depend strongly on whether the system is periodic if the system has enough solvent per image. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! GPG-ENCODED emails preferred !! pgp9L7YIPhODA.pgp Description: PGP signature ___ 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.
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Sorry I habe to extend this: Can you please explain me or provide am reference explain why I am not able to use a SPME/PME/PPPM/EwaldSum method for any kind of partial charges living in an environment with periodic boundary conditions ? When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity ... and assuming a homongenous medium beyond the boundaries. With the mentionend Ewald methods I should be able to reproduce exactly the same circumstances like in a reaction-field setup. So at the moment I can imagine just one critical point, when using SPME/PME/PPPM or an Ewald sum is the big set of parameters that have to adapted in Flo -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! pgpTuyKTWtM3E.pgp Description: PGP signature ___ 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] The Cut-off for coulombtype heat up the water system?
It is simply that if the system is not neutral the Ewald equation are not valid anymore. I would guess that the original papers describe it. I never looked into it. On Jun 19, 2009, at 21:02, Florian Dommert domm...@icp.uni- stuttgart.de wrote: * Mark Abraham mark.abra...@anu.edu.au [2009-06-19 14:55:02 +1000]: Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut- off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk = use multiple groups. = how ??? = I have been thinking that it is better to group the molecule = such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? = such as PME, PPPM ? = what's the suggestion about this? 3. Normally, how do people fix this problem? These days, PME will tend to be the easiest to defend in a publication. You will have lower heating problems with various modified forms of cut-offs and/or longer cut-offs, but then you have the problem of justifying the use of the force field, which was probably parametrized for some other coulomb scheme. Hi Mark, Can you please explain me or provide am reference explain why I am not able to use a SPME/PME/PPPM/EwaldSum method for any kind of partial charges living in an environment with periodic boundary conditions ? When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity != 1. With the mentionend Ewald methods I should be able to reproduce exactly the same circumstances like in a reaction-field setup. So at the moment I can imagine just one critical point, when using SPME/PME/PPPM or an Ewald sum is the big set of parameters that have to adapted in order to obtain an appropriate accuracy of the forces. In the reaction field method you just have two parameters: the cutoff and epsilon_r. The other algorithms require addtionally require the input of an appropriate size for used grid in Fourier space and in case of SPME/PME/PPPM also an interpolation order. Finally you need to set the splitting paramter correctly, otherwise you will obtain unaccurate forces. So there can be a very large error introduced, when applying the wrong parameters to the Ewald methods. The heat up of the water is also just related to extremly inaccurate electrostatic forces, since with PBC an infinite system is simulated and just a very small amount of the electrostatic interaction that is of long range nature is calculated. Therefore an large error is not unexpected. Finally the only restriction of Ewald I see is the requirement of PBC, where I can reach any level of accuracy for the electrostatic force given by certain charge distribution, don't I ? However I am always open to enhance my experience and knowledge therefore please let me know if understood anything wrong. Flo Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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] The Cut-off for coulombtype heat up the water system?
* XAvier Periole x.peri...@rug.nl [2009-06-20 00:45:55 +0200]: It is simply that if the system is not neutral the Ewald equation are not valid anymore. I would guess that the original papers describe it. I never looked into it. Thanks very much. This should really be the point, because a lattice built just of like-charged ions would have infinite energy. So this reason should suffice to explain why Ewald can not be applied in such cases. Flo On Jun 19, 2009, at 21:02, Florian Dommert domm...@icp.uni- stuttgart.de wrote: * Mark Abraham mark.abra...@anu.edu.au [2009-06-19 14:55:02 +1000]: Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut- off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk = use multiple groups. = how ??? = I have been thinking that it is better to group the molecule = such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? = such as PME, PPPM ? = what's the suggestion about this? 3. Normally, how do people fix this problem? These days, PME will tend to be the easiest to defend in a publication. You will have lower heating problems with various modified forms of cut-offs and/or longer cut-offs, but then you have the problem of justifying the use of the force field, which was probably parametrized for some other coulomb scheme. Hi Mark, Can you please explain me or provide am reference explain why I am not able to use a SPME/PME/PPPM/EwaldSum method for any kind of partial charges living in an environment with periodic boundary conditions ? When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity != 1. With the mentionend Ewald methods I should be able to reproduce exactly the same circumstances like in a reaction-field setup. So at the moment I can imagine just one critical point, when using SPME/PME/PPPM or an Ewald sum is the big set of parameters that have to adapted in order to obtain an appropriate accuracy of the forces. In the reaction field method you just have two parameters: the cutoff and epsilon_r. The other algorithms require addtionally require the input of an appropriate size for used grid in Fourier space and in case of SPME/PME/PPPM also an interpolation order. Finally you need to set the splitting paramter correctly, otherwise you will obtain unaccurate forces. So there can be a very large error introduced, when applying the wrong parameters to the Ewald methods. The heat up of the water is also just related to extremly inaccurate electrostatic forces, since with PBC an infinite system is simulated and just a very small amount of the electrostatic interaction that is of long range nature is calculated. Therefore an large error is not unexpected. Finally the only restriction of Ewald I see is the requirement of PBC, where I can reach any level of accuracy for the electrostatic force given by certain charge distribution, don't I ? However I am always open to enhance my experience and knowledge therefore please let me know if understood anything wrong. Flo Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Florian Dommert wrote: * Mark Abraham mark.abra...@anu.edu.au [2009-06-19 14:55:02 +1000]: Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk = use multiple groups. = how ??? = I have been thinking that it is better to group the molecule = such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? = such as PME, PPPM ? = what's the suggestion about this? 3. Normally, how do people fix this problem? These days, PME will tend to be the easiest to defend in a publication. You will have lower heating problems with various modified forms of cut-offs and/or longer cut-offs, but then you have the problem of justifying the use of the force field, which was probably parametrized for some other coulomb scheme. Hi Mark, Can you please explain me or provide am reference explain why I am not able to use a SPME/PME/PPPM/EwaldSum method for any kind of partial charges living in an environment with periodic boundary conditions ? I'm going to presume you mean a non-neutral charge instead of any kind of partial charges. Certainly Xavier's right, in that I've never seen an Ewald derivation that didn't start by assuming electric neutrality. Such a system would have an infinite potential, of course. The issue's been discussed on this list several times, and I don't recall any startling outcomes. Fortunately, there are likely to be very few biological systems where such neutrality is awkward to contrive. When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity != 1. With the mentionend Ewald methods I should be able to reproduce exactly the same circumstances like in a reaction-field setup. So at the moment I can imagine just one critical point, when using SPME/PME/PPPM or an Ewald sum is the big set of parameters that have to adapted in order to obtain an appropriate accuracy of the forces. In the reaction field method you just have two parameters: the cutoff and epsilon_r. The other algorithms require addtionally require the input of an appropriate size for used grid in Fourier space and in case of SPME/PME/PPPM also an interpolation order. Finally you need to set the splitting paramter correctly, otherwise you will obtain unaccurate forces. So there can be a very large error introduced, when applying the wrong parameters to the Ewald methods. The heat up of the water is also just related to extremly inaccurate electrostatic forces, since with PBC an infinite system is simulated and just a very small amount of the electrostatic interaction that is of long range nature is calculated. Therefore an large error is not unexpected. Finally the only restriction of Ewald I see is the requirement of PBC, where I can reach any level of accuracy for the electrostatic force given by certain charge distribution, don't I ? I really haven't understood you, sorry. However I am always open to enhance my experience and knowledge therefore please let me know if understood anything wrong. Indeed - I've always found that a key attribute in a research scientist. Mark ___ 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] The Cut-off for coulombtype heat up the water system?
* Mark Abraham mark.abra...@anu.edu.au [2009-06-20 11:54:46 +1000]: When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity != 1. With the mentionend Ewald methods I should be able to reproduce exactly the same circumstances like in a reaction-field setup. So at the moment I can imagine just one critical point, when using SPME/PME/PPPM or an Ewald sum is the big set of parameters that have to adapted in order to obtain an appropriate accuracy of the forces. In the reaction field method you just have two parameters: the cutoff and epsilon_r. The other algorithms require addtionally require the input of an appropriate size for used grid in Fourier space and in case of SPME/PME/PPPM also an interpolation order. Finally you need to set the splitting paramter correctly, otherwise you will obtain unaccurate forces. So there can be a very large error introduced, when applying the wrong parameters to the Ewald methods. The heat up of the water is also just related to extremly inaccurate electrostatic forces, since with PBC an infinite system is simulated and just a very small amount of the electrostatic interaction that is of long range nature is calculated. Therefore an large error is not unexpected. Finally the only restriction of Ewald I see is the requirement of PBC, where I can reach any level of accuracy for the electrostatic force given by certain charge distribution, don't I ? I really haven't understood you, sorry. I think that I a complete wrong idea of an simulation using a Reaction field, so I have to get a correct picture. Because when investigating a protein you require a physiological environment with corresponding ions to provide a certain pH value. Is this finally all contained in the force field parameters ? This would make things clear and enlight my foggy insight in this special way to treat electrostatic forces. Furthermore I assume no periodic boundary conditions are used then ? You just simulate a protein/polymer/molecule and assume that it is surrounded by a medium with a certain epsilon_r. Flo However I am always open to enhance my experience and knowledge therefore please let me know if understood anything wrong. Indeed - I've always found that a key attribute in a research scientist. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! GPG-ENCODED emails preferred !! pgpow4XEDHl2R.pgp Description: PGP signature ___ 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] The Cut-off for coulombtype heat up the water system?
Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] The Cut-off for coulombtype heat up the water system?
Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: That is correct. Check J. Chem. Theor. Comp. 2 (2006) p. 1-11. Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? That is one of the known problems with using cut-off, yes. -Justin On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Dear Justin: Thank you so much for your answer. That helps a lot! On Thu, Jun 18, 2009 at 10:35 AM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? That is one of the known problems with using cut-off, yes. -Justin On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin --Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post
[gmx-users] The Cut-off for coulombtype heat up the water system?
Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 1. From Berk = use multiple groups. = how ??? = I have been thinking that it is better to group the molecule = such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? = such as PME, PPPM ? = what's the suggestion about this? 3. Normally, how do people fix this problem? Thank you Lin http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html No, this problem is not due to the Berendsen thermostat. The integrations errors in the electrostatics have much more effect on the water than on the protein, because the water has higher charges and is far more mobile. No thermostat can correct for these errors, unless you use multiple groups. In addition the Berendsen thermostat will move energy from fast to slow motions. This effects becomes much stronger when the thermostat has to do a lot of scaling due to the heat generated by cut-off's. Inaccurate constraining will remove heat from the system, but this effect is orders of magnitude smaller than the Coulomb cut-off heating. Berk Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090618/08853d93/attachment.html ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] The Cut-off for coulombtype heat up the water system?
Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk = use multiple groups. = how ??? = I have been thinking that it is better to group the molecule = such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? = such as PME, PPPM ? = what's the suggestion about this? 3. Normally, how do people fix this problem? These days, PME will tend to be the easiest to defend in a publication. You will have lower heating problems with various modified forms of cut-offs and/or longer cut-offs, but then you have the problem of justifying the use of the force field, which was probably parametrized for some other coulomb scheme. Mark ___ 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] The Cut-off for coulombtype heat up the water system?
Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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] The Cut-off for coulombtype heat up the water system?
Yanmei Song wrote: Dear Users: I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics: title = water cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 50 ; total 8ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = Cut-off rlist = 0.8 rcoulomb= 0.9 rvdw= 0.8 fourierspacing = 0.12 ewald_rtol = 1e-5 ;nemd cos_acceleration= 0.005 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = SOL tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= SOL tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 I can not figure out where I did wrong, the temperature of the system is 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks for the help in advance! Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing: http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
