Re: [gmx-users] Nonbonded parameters
On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Nonbonded parameters
Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Nonbonded parameters
On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Nonbonded parameters
On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Nonbonded parameters
I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post
Re: [gmx-users] Nonbonded parameters
An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4 combinations so it should be lower than 1800... And why 1830 1-4 interactions as I have only 57... Please, help/ Steven On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann s.neuman...@gmail.comwrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing list
Re: [gmx-users] Nonbonded parameters
grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.comwrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
Re: [gmx-users] Nonbonded parameters
Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] Nonbonded parameters
All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ====
Re: [gmx-users] Nonbonded parameters
and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.comwrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin
Re: [gmx-users] Nonbonded parameters
How many atom *types* are there? On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.comwrote: and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.com wrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ====
Re: [gmx-users] Nonbonded parameters
60 types of atoms and 60 atoms in total belonging to one residue On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham mark.j.abra...@gmail.comwrote: How many atom *types* are there? On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.com wrote: and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.com wrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force
Re: [gmx-users] Nonbonded parameters
On 6/12/13 8:01 AM, Steven Neumann wrote: 60 types of atoms and 60 atoms in total belonging to one residue The number of possible combinations is (N(N+1))/2, thus you get 1830 from 60 atom types. -Justin On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham mark.j.abra...@gmail.comwrote: How many atom *types* are there? On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.com wrote: and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.com wrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem. vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Nonbonded parameters
So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Nonbonded parameters
On 6/12/13 8:16 AM, Steven Neumann wrote: So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions Mark already told you this - interactions that exist are different from possible interactions. You may have 57 interactions, but that's specific to your system because of how many atoms there are (which is also independent of how many atom types are used therein). grompp generates a bunch of information (a matrix of possible interactions that could theoretically occur with N atom types); whether or not it uses that information is not necessarily relevant. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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
