[gmx-users] Mu-X
Dear Users ! I have done the g_energy using the *.edr file ! In that it prints all the energy terms , i can understand most of the terms ! i dont know what does Mu-X , Mu-Y , Mu-Z represents and its importance ! I would like to know the detail of the force fields included in the gromacs ! is there any separate web for this ! thanks in advance ! -- 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] reg electrostatic potential
Dear justin Thank you for your previous reply. I would like to calculate absolute and cumulative value of electrostatic potential at specific distance from surfaces of particular group of my protein but g_potential calculates only across box also i would like to calculate vibrational entropy which tool is useful further i want to calculate mechanical stiffness of protein .is there is any tool in gromacs to find out stiffness I am expecting your reply Thanks in advance -- 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] g_sas calculation
Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a group: 2 (ligand) is this correct? *2.)* or g_sas -f run.xtc -s run.tpr -o protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2 (protein) I have protein SASA. g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg Select a group for calculation of surface and a group for output select a group: 1 (ligand) select a group: 2 (ligand) I have ligand SASA. protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein_ligand) select a group: 2 (protein_ligand) I have protein_ligand SASA. (SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand) I am confused. which of choices is correct? Thanks in advance -- Ahmet YILDIRIM -- 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] Mu-X
balaji nagarajan wrote: Dear Users ! I have done the g_energy using the *.edr file ! In that it prints all the energy terms , i can understand most of the terms ! i dont know what does Mu-X , Mu-Y , Mu-Z represents and its importance ! Dipole information in the x, y, and z dimensions. I would like to know the detail of the force fields included in the gromacs ! is there any separate web for this ! Nothing comprehensive. You're better off reading the primary citations for whatever force field(s) you're interested in. -Justin -- 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
Re: [gmx-users] g_sas calculation
ahmet yıldırım wrote: Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a group: 2 (ligand) is this correct? *2.)* or g_sas -f run.xtc -s run.tpr -o protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2 (protein) I have protein SASA. g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg Select a group for calculation of surface and a group for output select a group: 1 (ligand) select a group: 2 (ligand) I have ligand SASA. protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein_ligand) select a group: 2 (protein_ligand) I have protein_ligand SASA. (SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand) I am confused. which of choices is correct? Neither. Your equation is right, but your method of calculating each of the quantities is not. The group for the surface calculation should always be all non-solvent atoms (per the instructions in g_sas -h). The output group can then be whatever you like, a subset of that surface. So you will need three calculations (sort of like option #2), but in each case the calculation group should always be the protein-ligand merged group. -Justin -- 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
Re: [gmx-users] reg electrostatic potential
vidhya sankar wrote: Dear justin Thank you for your previous reply. I would like to calculate absolute and cumulative value of electrostatic potential at specific distance from surfaces of particular group of my protein but g_potential calculates only across box Can't you do this by analyzing each axis separately? If you center the protein in the box, it should give you some sort of useful information. Otherwise maybe try the -spherical option. I don't know if it will do what you want, but it sounds close. also i would like to calculate vibrational entropy which tool is useful Maybe g_anaeig (which also means running g_covar first). further i want to calculate mechanical stiffness of protein .is there is any tool in gromacs to find out stiffness Not likely. You can determine flexibility of residues with g_rmsf, but not mechanical stiffness. Without some applied deformation, I don't know how you'd quantify this. -Justin -- 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
Re: [gmx-users] g_sas calculation
Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein)* *I have protein SASA.* g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (ligand) I have ligand SASA.* g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein_ligand) I have protein_ligand SASA.* *(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)* Thanks 2011/7/3 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a group: 2 (ligand) is this correct? *2.)* or g_sas -f run.xtc -s run.tpr -o protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2 (protein) I have protein SASA. g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg Select a group for calculation of surface and a group for output select a group: 1 (ligand) select a group: 2 (ligand) I have ligand SASA. protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein_ligand) select a group: 2 (protein_ligand) I have protein_ligand SASA. (SASA between protein and ligand)=(protein)+(ligand)-(**protein_ligand) I am confused. which of choices is correct? Neither. Your equation is right, but your method of calculating each of the quantities is not. The group for the surface calculation should always be all non-solvent atoms (per the instructions in g_sas -h). The output group can then be whatever you like, a subset of that surface. So you will need three calculations (sort of like option #2), but in each case the calculation group should always be the protein-ligand merged group. -Justin -- ==**== 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/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 -- Ahmet YILDIRIM -- 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] g_sas calculation
ahmet yıldırım wrote: Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein)* *I have protein SASA.* g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (ligand) I have ligand SASA.* g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein_ligand) I have protein_ligand SASA.* *(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)* I'm sorry, I read the first post wrong. Your equation will yield an answer of zero if you do this. I was thinking of your problem backwards. You do indeed want to calculate all of these quantities individually, as you proposed in method #2 previously. That way, you can get the interior cavity surface area, not the exterior components as I was thinking. -Justin Thanks 2011/7/3 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu ahmet yıldırım wrote: Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a group: 2 (ligand) is this correct? *2.)* or g_sas -f run.xtc -s run.tpr -o protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2 (protein) I have protein SASA. g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg Select a group for calculation of surface and a group for output select a group: 1 (ligand) select a group: 2 (ligand) I have ligand SASA. protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein_ligand) select a group: 2 (protein_ligand) I have protein_ligand SASA. (SASA between protein and ligand)=(protein)+(ligand)-(__protein_ligand) I am confused. which of choices is correct? Neither. Your equation is right, but your method of calculating each of the quantities is not. The group for the surface calculation should always be all non-solvent atoms (per the instructions in g_sas -h). The output group can then be whatever you like, a subset of that surface. So you will need three calculations (sort of like option #2), but in each case the calculation group should always be the protein-ligand merged group. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- 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
Re: [gmx-users] g_sas calculation
Justin A. Lemkul wrote: ahmet yıldırım wrote: Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein)* *I have protein SASA.* g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (ligand) I have ligand SASA.* g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein_ligand) I have protein_ligand SASA.* *(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)* I'm sorry, I read the first post wrong. Your equation will yield an answer of zero if you do this. I was thinking of your problem backwards. You do indeed want to calculate all of these quantities individually, as you proposed in method #2 previously. That way, you can get the interior cavity surface area, not the exterior components as I was thinking. In addition, this gives the buried surface area, which is actually twice the interfacial surface area. Both can be useful to understand (the former for analyzing the free energy change of burying these surfaces and the latter for the actual level of contact between the protein and ligand). -Justin -- 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] On multi-core PCs and gromacs installation
Hi everyone! I will be installing gromacs 4.5.x in another computer but this time with four cores. The PC runs in windows and I will be using cygwin. The instructions says: If you want to run in parallel across a network, you need MPI. If you are running on a supercomputer you probably already have an optimized MPI version installed - consult your documentation or ask your system administrator. See below for information about how to make use of MPI. As of GROMACS 4.5, threading is supported, so for e.g multi-core workstations, MPI is no longer required The last note says that I do not have to install MPI. Do I still need to install MPI using cygwin? Or cygwin/windows will do the MPI for me. Thanks. -- 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] On multi-core PCs and gromacs installation
On 4/07/2011 2:54 PM, Mr Bernard Ramos wrote: Hi everyone! I will be installing gromacs 4.5.x in another computer but this time with four cores. The PC runs in windows and I will be using cygwin. The instructions says: If you want to run in parallel across a network, you need MPI. If you are running on a supercomputer you probably already have an optimized MPI version installed - consult your documentation or ask your system administrator. See below for information about how to make use of MPI. /As of GROMACS 4.5, threading is supported, so for e.g multi-core workstations, MPI is no longer required/ The last note says that I do not have to install MPI. Do I still need to install MPI using cygwin? Probably not, but I haven't tested threading on Cygwin. Or cygwin/windows will do the MPI for me. Nothing will do MPI for you. Threading and MPI are complementary approaches to achieving parallelism, and which is better depends on your execution environment. 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/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] final_min_step energy
Dear Users ! I have a problem in taking the inter and intra molecular interaction energy from a pdb , which is being minimized by minim.mdp ! when i use the g_energy -f *.edr it gives the list of all possible interaction energy as average value , but i want it only for the minimized file how one can fetch that from the *.edr file thanks in advance -- 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
