Re: [gmx-users] Settle vs. 3 normal constraints
Hi, Using normal constraint algorithms with triangles of constraints can be tricky with some integrators. Do check out the several manual sections that talk about how these algorithms work, e.g. you may need to increase lincs-order Mark On Wed, Jul 29, 2015 at 5:47 PM Andreas Mecklenfeld a.mecklenf...@tu-braunschweig.de wrote: Dear GROMACS users, I want to calculate the solvation free energy of a rigid water molecule, e.g. TIP4P-Ew. To do this, I define one solute molecule which I refer to as couple-moltype in the .mdp-file (SOL). The solvens molecules are exactly the same, just named differently for distinction (SOLB). Since I can't simulate two molecule types with settle, I want to use constraints. My .itp-file looks like this: ; ; tip4pew Water model ; [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW_tip4pew 1 SOL OW 1 0 16.0 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 4 MW1 SOL MW 1 -1.04844 0.0 [ constraints ] 1210.09572; func. 1: chemical bond (O-H) 1310.09572; func. 1: chemical bond (O-H) 2320.15139; func. 2: no chemical bond (H-H) [ virtual_sites3 ] ; Vsite from funct a b 4 1 2 3 1 0.106676721 0.106676721 [ exclusions ] 1234 2134 3124 4123 ; The position of the virtual site is computed as follows: ; ; O ; ; V ; ;HH ; ; Ewald tip4p: ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] ; 0.0125 nm/ [ cos (52.26 deg)* 0.09572 nm] ;then a = b = 0.5 * const = 0.106676721 ; ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) The temperature derivates by 20 K using the sd-intergrator as thermostat. By using the settle algorithm for only one molecule (same .mdp and .gro files as for the constrained), I gain results as expected. I'm sorry if this is a trivial question. Thanks for your support! Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Settle vs. 3 normal constraints
Dear Mark, thanks a lot for this advice - I've changed my .mdp to lincs-order = 8 and it works just fine! Andreas Am 30.07.2015 um 13:59 schrieb Mark Abraham: Hi, Using normal constraint algorithms with triangles of constraints can be tricky with some integrators. Do check out the several manual sections that talk about how these algorithms work, e.g. you may need to increase lincs-order Mark On Wed, Jul 29, 2015 at 5:47 PM Andreas Mecklenfeld a.mecklenf...@tu-braunschweig.de wrote: Dear GROMACS users, I want to calculate the solvation free energy of a rigid water molecule, e.g. TIP4P-Ew. To do this, I define one solute molecule which I refer to as couple-moltype in the .mdp-file (SOL). The solvens molecules are exactly the same, just named differently for distinction (SOLB). Since I can't simulate two molecule types with settle, I want to use constraints. My .itp-file looks like this: ; ; tip4pew Water model ; [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW_tip4pew 1 SOL OW 1 0 16.0 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 4 MW1 SOL MW 1 -1.04844 0.0 [ constraints ] 1210.09572; func. 1: chemical bond (O-H) 1310.09572; func. 1: chemical bond (O-H) 2320.15139; func. 2: no chemical bond (H-H) [ virtual_sites3 ] ; Vsite from funct a b 4 1 2 3 1 0.106676721 0.106676721 [ exclusions ] 1234 2134 3124 4123 ; The position of the virtual site is computed as follows: ; ; O ; ; V ; ;HH ; ; Ewald tip4p: ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] ; 0.0125 nm/ [ cos (52.26 deg)* 0.09572 nm] ;then a = b = 0.5 * const = 0.106676721 ; ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) The temperature derivates by 20 K using the sd-intergrator as thermostat. By using the settle algorithm for only one molecule (same .mdp and .gro files as for the constrained), I gain results as expected. I'm sorry if this is a trivial question. Thanks for your support! Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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. -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Settle vs. 3 normal constraints
Dear GROMACS users, I want to calculate the solvation free energy of a rigid water molecule, e.g. TIP4P-Ew. To do this, I define one solute molecule which I refer to as couple-moltype in the .mdp-file (SOL). The solvens molecules are exactly the same, just named differently for distinction (SOLB). Since I can't simulate two molecule types with settle, I want to use constraints. My .itp-file looks like this: ; ; tip4pew Water model ; [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW_tip4pew 1 SOL OW 1 0 16.0 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 4 MW1 SOL MW 1 -1.04844 0.0 [ constraints ] 1210.09572; func. 1: chemical bond (O-H) 1310.09572; func. 1: chemical bond (O-H) 2320.15139; func. 2: no chemical bond (H-H) [ virtual_sites3 ] ; Vsite from funct a b 4 1 2 3 1 0.106676721 0.106676721 [ exclusions ] 1234 2134 3124 4123 ; The position of the virtual site is computed as follows: ; ; O ; ; V ; ;HH ; ; Ewald tip4p: ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] ; 0.0125 nm/ [ cos (52.26 deg)* 0.09572 nm] ;then a = b = 0.5 * const = 0.106676721 ; ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) The temperature derivates by 20 K using the sd-intergrator as thermostat. By using the settle algorithm for only one molecule (same .mdp and .gro files as for the constrained), I gain results as expected. I'm sorry if this is a trivial question. Thanks for your support! Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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.
