Re: [gmx-users] Position restraints with multiple identical molecules
Hi Justin, Ok - the .tpr file only lists the atoms from the molecule type. I get it now. Thanks again! Craig On 16 Jun 2011, at 12:58, Justin A. Lemkul wrote: Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include "posre.itp" #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 -- 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] Position restraints with multiple identical molecules
You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that >contains it, so if you only have one [moleculetype] then any instance of it will have the restraint >applied to whatever atoms are indicated. -Justin Hi Justin, thanks for your reply. If this is the case then should I not expect to see all the position restraints in the .tpr file? Using gmxdump -s md1.tpr to inspect the file I can only see Position Rest.: nr: 2 iatoms: 0 type=1 (POSRES) 0 (this is on the simplified 5 atom case). Which implies there is one position restraint on atom 1 (index 0 I guess). Craig Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include "posre.itp" #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 -- 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] Position restraints with multiple identical molecules
Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include "posre.itp" #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] Position restraints with multiple identical molecules
Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include "posre.itp" #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading "91 1 2000 2000 2000" gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- 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
