Re: [gmx-users] energy_terms
balaji nagarajan wrote: 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 Bonded terms cannot be decomposed for systems composed of different types of molecules. I believe what was suggested was to use tpbconv and trjconv to create trajectories with subsets of the system (for instance, the protein alone) which can be processed with mdrun -rerun to recalculate bonded interactions, which will now correspond to only the molecule(s) present. Use of rigid water (standard) or constraints on bonds (also typical) removes some bonded terms in favor of constraint RMSD terms. -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] energy_terms
On 18/12/2011 11:28 AM, Mark Abraham wrote: On 18/12/2011 3:56 AM, balaji nagarajan wrote: 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 . You can't do this during the original simulation, but you can take a completed simulation and use tpbconv on the .tpr and trjconv on the trajectory file to extract the same subset of atoms from each. Now mdrun -rerun on those two partial files can give you the bonded energies of whatever interests you. Whether that bond energy means anything is another matter. Of course, if you used a rigid water molecule for the simulation, then there are already no bonded contributions from water. Mark Mark 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 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] energy_terms
On 18/12/2011 3:56 AM, balaji nagarajan wrote: 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 . You can't do this during the original simulation, but you can take a completed simulation and use tpbconv on the .tpr and trjconv on the trajectory file to extract the same subset of atoms from each. Now mdrun -rerun on those two partial files can give you the bonded energies of whatever interests you. Whether that bond energy means anything is another matter. Mark 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 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] 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
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
