[gmx-users] how to get a minimized structure pdb
Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below trjconv -f em.trr -o min.pdb -s em.tpr EOF 0 EOF the out put pdb has many structures as follows MODEL 0 MODEL 1 MODEL 2 but the minimized pdb is single structre , what does these structures mean. how to obtain a single structre. my mimization input file is as follows -- define = -DFLEXIBLE constraints = none integrator = cg dt = 0.001 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 optimize_fft = yes ; ;Energy minimizing stuff ; emtol= 10.0 emstep = 0.01 energygrps = protein SOL 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] how to get a minimized structure pdb
Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below trjconv -f em.trr -o min.pdb -s em.tpr EOF 0 EOF the out put pdb has many structures as follows MODEL 0 MODEL 1 MODEL 2 but the minimized pdb is single structre , what does these structures mean. how to obtain a single structre. my mimization input file is as follows -- define = -DFLEXIBLE constraints = none integrator = cg dt = 0.001 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 optimize_fft = yes ; ;Energy minimizing stuff ; emtol= 10.0 emstep = 0.01 energygrps = protein SOL thanks in advance Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below trjconv -f em.trr -o min.pdb -s em.tpr EOF 0 EOF the out put pdb has many structures as follows MODEL 0 MODEL 1 MODEL 2 but the minimized pdb is single structre , what does these structures mean. how to obtain a single structre. my mimization input file is as follows -- define = -DFLEXIBLE constraints = none integrator = cg dt = 0.001 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 optimize_fft = yes ; ;Energy minimizing stuff ; emtol= 10.0 emstep = 0.01 energygrps = protein SOL 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] energy_terms
Dear Users I have a peptide, (1AKI.pdb) My aim is to solvate it in the presence of the explicit water molecules and do minimization and to split the energy terms , and to see the energy contribution from each terms for this i have done the following in gromacs --- pdb2gmx -ignh -ff gromos43a1 -f 1AKI.pdb -o 1AKI_processed.gro -water spc editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr mdrun -v -deffnm em the minim.mdp file is as follows --- define = -DFLEXIBLE constraints = none integrator = cg dt = 0.001 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 optimize_fft = yes ; ;Energy minimizing stuff ; emtol= 10.0 emstep = 0.01 energygrps = protein SOL in the above i have given the energy groups, protein and solvent after minimization one can get the energy values from all the possible contributions as follows g_energy -f em.edr in this term it is not possible to separate the bond distance and the bond angle term for the protein and water separately, How to get these terms separately for water and the protein for this minimized structure ? ( for a single structure) I can not under stand the earlier explanation , could any one can tell in detail 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
RE: [gmx-users] energy_terms
Dear Users ! I can print the values of the bonded and non bonded energy terms of the protein and the water , I have used the group option , I want to know the bonded contribution only from the protein , in case of the torsion energy term it is only for the protein , The bond distance and the bond angle , the contribution from the water is also there , so how one can get these terms for protein alone . thanks in advance Date: Sat, 17 Dec 2011 17:39:47 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] energy_terms On 17/12/2011 5:25 PM, balaji nagarajan wrote: Dear Users ! I have used the energy group option to split the energy terms , for the protein and the water. You have split the *non-bonded* terms. It gives all the terms , protein-protein , water-water , water-protein . I have a doubt , the distance and the angle are taken for both water and the protein , I don't see what distance and angle you mean. how one can get these energy terms for protein alone. What energy terms do you want? You have the intra-protein non-bonded energies above. 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 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] energy_terms
Dear Users ! I have used the energy group option to split the energy terms , for the protein and the water. It gives all the terms , protein-protein , water-water , water-protein . I have a doubt , the distance and the angle are taken for both water and the protein , how one can get these energy terms for protein alone. 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] error_in topology
Dear Users ! I have a problem in generating the topology of the attached molecule as pdb. earlier i have done using the same pdb for solvating the structure using spc and spce water box , there was no such error when i do for TIP4P and oplsaa force field i got the error as follows --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (1AKI_solv.gro, 4164) does not match topology (topol.top, 5527) I used the following lines to do that pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr mdrun -v -deffnm em in the grompp it says the error , how to solve this , and it comes only for tip4p not for other water models. thanks in advance 1AKI.pdb Description: application/aportisdoc -- 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] topology_for_3 point model
Dear Users ! Thanks for the mail , now i fixed it i have a general doubt, i saw the path of gromacs /usr/local/gromacs-4.5.3/share/top there for the three point water model only spc216.gro is there is this common for all , ie ., spc , spc/e and tip3p. Date: Mon, 10 Oct 2011 07:02:04 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] error_in topology balaji nagarajan wrote: Dear Users ! I have a problem in generating the topology of the attached molecule as pdb. earlier i have done using the same pdb for solvating the structure using spc and spce water box , there was no such error when i do for TIP4P and oplsaa force field i got the error as follows --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (1AKI_solv.gro, 4164) does not match topology (topol.top, 5527) I used the following lines to do that pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top You told pdb2gmx to write the TIP4P topology into your .top, but then you used a 3-point water model. You need to solvate with tip4p.gro. -Justin grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr mdrun -v -deffnm em in the grompp it says the error , how to solve this , and it comes only for tip4p not for other water models. thanks in advance -- 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 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] problem_with_rewritting_pdb
Dear Users ! I have minimized the attached file using the gromacs43a1 and oplsaa force field using spc water molecules I have used the following script for generating topology . i minimized for 2000 steps , my doubt is when i rewrite the minimized pdb , in case of oplsaa i was able to get all atoms , but in the case of the gromacs43a1 i am not getting the hydrogen atoms of the protein , how to solve this here is the steps which i have used --- pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water spc editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr mdrun -v -deffnm em trjconv -f em.trr -o min.pdb -s em.tpr ( in this i gave the option 0 for the total system) -- the minim.mdp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 optimize_fft = yes ; ;Energy minimizing stuff ; emtol= 10.0 emstep = 0.01 --- thanks in advance 1AKI.pdb Description: application/aportisdoc -- 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] free energy
Dear Users ! Is it possible to calculate the free energy for a molecule , at the zero step MD , when i see the mail list this question has been posted once , but i could not find the reply for this ! is there any option for this like g_energy ! -- 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] minimization_error
Dear Users ! I have a doubt in minimizing the structure with water box ! I have taken a penta peptide and solvated it with spce water box ! I have minimized the system with the minim.mdp file which i have attached ! ( i have used steep option ) when I calculated the protein- protein and protein-solvent interaction energy the protein-protein energy have not fall down much ! and i tried with various options in the mdp options emtol (how to know that the system is entirely minimized ! what is the criteria to be fixed on regarding a small peptide ) when i have the option 6 of the file ( Coulomb-14 ) for the first step and the last step ! Statistics over 1 steps [ 0. through 0. ps ], 1 data sets All statistics are over 1 points Energy Average Err.Est. RMSD Tot-Drift --- Coulomb-14 908.433 -- 0 0 (kJ/mol) Statistics over 1000 steps [ 0. through 999. ps ], 1 data sets All statistics are over 2 points Energy Average Err.Est. RMSD Tot-Drift --- Coulomb-14892.22.3nan -16.4675 (kJ/mol) I have attached all the files below ! the script test-script.sh is to run all which i have done ! thanks in advance files.tar.gz Description: GNU Zip compressed data -- 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] 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] 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
[gmx-users] energy_extract
Dear Users ! I have took a penta peptide and did topology generation , I have solvated it with water box , now i did a minimization with zero step , to know the energy of the initial molecule , i used g_energy for the out put , like $ g_energy -f em.edr it gives as follows , i have to type number to get energy ! but it lists Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. --- 1 Bond 2 Angle3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y34 Mu-Z35 T-rest Is there any way to get the energy of the protein and the energy of protein and water alone I dont need water water interactions ! how to do 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] solvent_protein interaction energy
Thanks for the reply ! I have tried building the topology with generating the index file make_ndx -f * it gave options i have selected the protein and the solvent then i gave minimization in the minimization file i have included energygrps = Protein SOL , but the energy file have the same when i removed and inserted the above flag ! if any one can explain me in detail it will be helpfull 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] interaction energy
Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a 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
RE: [gmx-users] interaction energy
Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in g_energy , thanks in advance Date: Fri, 1 Jul 2011 13:40:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! As prompted by g_energy: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. Writing all terms to the same output file will result in nothing but an incoherent mess. Choose terms wisely based on what you actually need to analyze. -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 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] interaction energy
Dear users ! thanks for the reply I was able to do that , otherwise we can select the number of the option one by one and enter then after that if we leave a empty line and enter it gives all the needed energy terms ! my intension is not to do like this is it possible to give it along the g_energy like g_energy -f em.edr --- ( any options can be given along with this , i tried g_energy -f em.edr 11 0 ( it is not working ) how it can be done ? Date: Fri, 1 Jul 2011 13:53:59 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in I quoted the help description for how to do this. Is there some problem? For instance, if you want to write the potential energy to an .xvg file, type: 11 0 and hit Enter. The values will be printed. -Justin g_energy , thanks in advance Date: Fri, 1 Jul 2011 13:40:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] interaction energy balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR) 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X 33 Mu-Y 34 Mu-Z 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL 49 LJ-14:SOL-SOL 50 T-rest --- how one can write this all to a file ! As prompted by g_energy: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. Writing all terms to the same output file will result in nothing but an incoherent mess. Choose terms wisely based on what you actually need to analyze. -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 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 -- 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 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] terminal_fixing
Dear Users ! i have tried in generating the -ter option in generating the topology file ! it asks the below if i give the ter option , Select start terminus type for TYR-1 0: NH3+ 1: ZWITTERION_NH3+ 2: NH2 3: None then if i give option 1 it chooses ZWITTERION_NH3+ , i want to make the charge state of the protein as ZWITTERION , in terminal how to do it in command mode thanks in advance balaji -- 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] print inter and intra energy
Dear users ! I am new to gromacs ! I have installed the package ! and it is working fine ! I tried to solvate a peptide and i was able to select the force field of my interest , I would like to calculate the energy of the structure in terms of inter and intra and i want to print all the components of the energy both non bonded and bonded. like , i have solvated a peptide , now could i able to print the inter and intra energy of the same with out doing minimization in gromacs ! thanks in advance ! regards balaji -- 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
