[gmx-users] Re: angle constraints
Thanks for the clarification. Forgot that virtual sites have no mass. With this info it is clear why a setup with 2 'normal' and one dummy atom would not work. Am 26.07.2012 01:42, schrieb gmx-users-requ...@gromacs.org: On 26/07/2012 4:12 AM, Broadbent, Richard wrote: Virtual sites are by definition have no mass. If you simply ignore the mass of the carbon the molecule will be too light and its translational momentum will therefore be too small meaning it will move too quickly. If you place half the mass of the carbon on each oxygen the moment of inertia will be wrong and the molecule will spin too slowly. All correct so far. In practice you have to decide what you want to loose or if a balance between the two is better. Not true, as illustrated by the link I gave earlier in the thread, which nobody seems to have read/understood. One needs at least two massive particles to describe the available degrees of freedom of a linear molecule, and using exactly two side-steps the angle constraint issue. Each must have half the total mass of CO2 and the distance between them is chosen to reproduce the moment of inertia. These will not be in suitable positions to have non-bonded interactions, of course. Then three (massless) virtual sites are constructed from those two, and these are the only ones that have the non-bonded interactions. Richard On 25/07/2012 14:44, Thomas Schlesierschl...@uni-mainz.de wrote: Ok, read the topic about the acetonitril. But i'm somewhat clueless: Why is the following setup wrong: Use 2 particles as normal atoms. Put the third as a dummy in between. Give each particle its 'normal' mass? I would assume that this system should have the right mass and moment of inertia, due to the fact the all individual masses and the positions one the particles would be correct. The virtual site so constructed cannot have mass, so this cannot be an accurate model. Only idea i have, why this setup could be flawed, would be that the third particle does only interact indirectly through the other two particles (i mean, virtual site interacts normally with all othe particles, but the force which would act on the dummy get redistributed to the other particles)... and then it's mass does not come into play, since it new position is determined only by the other two particles. so the complete molecule would move with a reduced mass?!? Still not an accurate model - you'd have a CO2 with three sites and mass only at two of the sites, so either the mass or moment of intertia must be wrong. Mark Can anyone comment on this? greetings thomas On 25/07/2012 10:08 PM, Thomas Schlesier wrote: What you have done there looks very strange... easiest wy would be: define the two oxygens as normal atoms (1,2), give them a bondlength twotimes the C-O bond length define the carbon as a dummy (3), while you construct it's position from both oxygens with a=0.5 one thing i don't know is how to handle the mass: 1) give both oxygen half of the system mass 2) give all atoms their normal mass would tend to (2) One should want to get both the total mass and the moment of inertia correct... http://lists.gromacs.org/pipermail/gmx-users/2003-September/007095.html. Mark greetings thomas Am 25.07.2012 13:15, schrieb gmx-users-request at gromacs.org: How to choose the positions of the dummy atoms while constraining the angle for a linear triatomic molecule? The topology for a such molecule ( af for example CO2 ) is as follows [ moleculetype ] ; Namenrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 503 CO rtp CO q 0.0 1 D1503 CO D1 1 0 21.90158 ; qtot 0 2 D2503 CO D2 2 0 21.90158 ; qtot 0 3 CE503 CO CO 30.7 0.0 ; qtot 0.7 4 OE503 COOC1 4 -0.35 0.0 ; qtot 0.35 5 OE503 COOC2 5 -0.35 0.0 ; qtot 0.35 [ constraints ] ; ai aj funct b0 1 2 1 0.2000 [ dummies2 ] ; aiajak funct a 3 1 2 1 0.0170 4 1 2 1 0.1000 5 1 2 1 0.2170 [ exclusions ] 3 4 5 4 5 3 5 4 3 The .rtp file for CO2 [ CO ] [ atoms ] D1 D1 0. 1 D2 D2 0. 2 COCE 0.70003 OC1 OE -0.3500 4 OC2 OE -0.35005 [ bonds ] CO OC1 CO OC2 Can anyone please check above file parts whether I'm doing correct or not ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
[gmx-users] Re: angle constraints
What you have done there looks very strange... easiest wy would be: define the two oxygens as normal atoms (1,2), give them a bondlength twotimes the C-O bond length define the carbon as a dummy (3), while you construct it's position from both oxygens with a=0.5 one thing i don't know is how to handle the mass: 1) give both oxygen half of the system mass 2) give all atoms their normal mass would tend to (2) greetings thomas Am 25.07.2012 13:15, schrieb gmx-users-requ...@gromacs.org: How to choose the positions of the dummy atoms while constraining the angle for a linear triatomic molecule? The topology for a such molecule ( af for example CO2 ) is as follows [ moleculetype ] ; Namenrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 503 CO rtp CO q 0.0 1 D1503 CO D1 1 0 21.90158 ; qtot 0 2 D2503 CO D2 2 0 21.90158 ; qtot 0 3 CE503 CO CO 30.7 0.0 ; qtot 0.7 4 OE503 COOC1 4 -0.35 0.0 ; qtot 0.35 5 OE503 COOC2 5 -0.35 0.0 ; qtot 0.35 [ constraints ] ; ai aj funct b0 1 2 1 0.2000 [ dummies2 ] ; aiajak funct a 3 1 2 1 0.0170 4 1 2 1 0.1000 5 1 2 1 0.2170 [ exclusions ] 3 4 5 4 5 3 5 4 3 The .rtp file for CO2 [ CO ] [ atoms ] D1 D1 0. 1 D2 D2 0. 2 COCE 0.7000 3 OC1 OE -0.35004 OC2 OE -0.35005 [ bonds ] CO OC1 CO OC2 Can anyone please check above file parts whether I'm doing correct or not ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: angle constraints
On 25/07/2012 10:08 PM, Thomas Schlesier wrote: What you have done there looks very strange... easiest wy would be: define the two oxygens as normal atoms (1,2), give them a bondlength twotimes the C-O bond length define the carbon as a dummy (3), while you construct it's position from both oxygens with a=0.5 one thing i don't know is how to handle the mass: 1) give both oxygen half of the system mass 2) give all atoms their normal mass would tend to (2) One should want to get both the total mass and the moment of inertia correct... http://lists.gromacs.org/pipermail/gmx-users/2003-September/007095.html. Mark greetings thomas Am 25.07.2012 13:15, schrieb gmx-users-requ...@gromacs.org: How to choose the positions of the dummy atoms while constraining the angle for a linear triatomic molecule? The topology for a such molecule ( af for example CO2 ) is as follows [ moleculetype ] ; Namenrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 503 CO rtp CO q 0.0 1 D1503 CO D1 1 0 21.90158 ; qtot 0 2 D2503 CO D2 2 0 21.90158 ; qtot 0 3 CE503 CO CO 30.7 0.0 ; qtot 0.7 4 OE503 COOC1 4 -0.35 0.0 ; qtot 0.35 5 OE503 COOC2 5 -0.35 0.0 ; qtot 0.35 [ constraints ] ; ai aj funct b0 1 2 1 0.2000 [ dummies2 ] ; aiajak funct a 3 1 2 1 0.0170 4 1 2 1 0.1000 5 1 2 1 0.2170 [ exclusions ] 3 4 5 4 5 3 5 4 3 The .rtp file for CO2 [ CO ] [ atoms ] D1 D1 0. 1 D2 D2 0. 2 COCE 0.70003 OC1 OE -0.3500 4 OC2 OE -0.35005 [ bonds ] CO OC1 CO OC2 Can anyone please check above file parts whether I'm doing correct or not ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: angle constraints
As others said: type 2 virtual site check chapter 4.7 and 5.2.2 in the manual (version 4.5.x). Greetings Thomas Am 24.07.2012 12:00, schrieb gmx-users-requ...@gromacs.org: Sorry I should mention it at the very beginning that I have a linear molecule and the angle is to be constrained at 180 degree. So what is the best way of constraining the angle for the linear molecule ? On Tue, Jul 24, 2012 at 2:06 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 6:07 PM, Broadbent, Richard wrote: An Angle constraint amounts to fixing a triangle. To do this you need to constrain the distances between all the atoms as you know the of the bonds 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a trivial geometry problem calculate the length of the third side of the triangle (6064,6065). However, as you are attempting to hold these atoms in a straight line I would suggest that a type 2 virtual site might (depending on your system) be a better idea. Indeed, a much better idea. Mark Richard On 24/07/2012 07:21, tarak karmakartarak20...@gmail.com wrote: Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website athttp://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- gmx-users mailing listgmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it togmx-users-requ...@gromacs.org. * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it togmx-users-requ...@gromacs.org. * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: angle constraints
How to choose the positions of the dummy atoms while constraining the angle for a linear triatomic molecule? The topology for a such molecule ( af for example CO2 ) is as follows [ moleculetype ] ; Namenrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 503 CO rtp CO q 0.0 1 D1503 CO D1 1 0 21.90158 ; qtot 0 2 D2503 CO D2 2 0 21.90158 ; qtot 0 3 CE503 CO CO 30.7 0.0 ; qtot 0.7 4 OE503 COOC1 4 -0.35 0.0 ; qtot 0.35 5 OE503 COOC2 5 -0.35 0.0 ; qtot 0.35 [ constraints ] ; ai aj funct b0 1 2 1 0.2000 [ dummies2 ] ; aiajak funct a 3 1 2 1 0.0170 4 1 2 1 0.1000 5 1 2 1 0.2170 [ exclusions ] 3 4 5 4 5 3 5 4 3 The .rtp file for CO2 [ CO ] [ atoms ] D1 D1 0. 1 D2 D2 0. 2 COCE 0.70003 OC1 OE -0.3500 4 OC2 OE -0.3500 5 [ bonds ] COOC1 COOC2 Can anyone please check above file parts whether I'm doing correct or not ? On Tue, Jul 24, 2012 at 4:25 PM, Thomas Schlesier schl...@uni-mainz.de wrote: As others said: type 2 virtual site check chapter 4.7 and 5.2.2 in the manual (version 4.5.x). Greetings Thomas Am 24.07.2012 12:00, schrieb gmx-users-requ...@gromacs.org: Sorry I should mention it at the very beginning that I have a linear molecule and the angle is to be constrained at 180 degree. So what is the best way of constraining the angle for the linear molecule ? On Tue, Jul 24, 2012 at 2:06 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 6:07 PM, Broadbent, Richard wrote: An Angle constraint amounts to fixing a triangle. To do this you need to constrain the distances between all the atoms as you know the of the bonds 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a trivial geometry problem calculate the length of the third side of the triangle (6064,6065). However, as you are attempting to hold these atoms in a straight line I would suggest that a type 2 virtual site might (depending on your system) be a better idea. Indeed, a much better idea. Mark Richard On 24/07/2012 07:21, tarak karmakartarak20...@gmail.com wrote: Oh ! Thnaks I saw that table, the angle_restrain option is there but not constraints . Anyway if suppose, I fix the distance between the two terminal atoms of the molecule, the angle will eventually be fixed at a particular given value. Is that the logic ? Actually I searched for this problem so many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abrahammark.abra...@anu.edu.au wrote: On 24/07/2012 3:21 PM, tarak karmakar wrote: Dear All, I am constraining one angle in my protein sample by incorporating [ constraints ] block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Source code file: topdirs.c, line: 174 Fatal error: Invalid constraints type 6065 For more information and tips for troubleshooting, please check the GROMACS website athttp://www.gromacs.org/Documentation/Errors As you will see in table 5.6, this is not a valid option for [constraints] - you can only specify bonds. You will need to construct a triangle of bond constraints. Mark Then I rechecked the angle block, that specific angle is there in that angle section, part of it as follows 6039 6057 6058 1 6039 6057 6059 1 6058 6057 6059 1 6064 6063 6065 1 6067 6066 6068 1 6067 6066 6069 1 6068 6066 6069 1 6071 6070 6072 1 6071 6070 6073 1 6072 6070 6073 1 [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 [ dihedrals ] ; aiajakal functc0c1 c2c3c4 -- gmx-users mailing listgmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it togmx-users-requ...@gromacs.org. * Can't post?
