Re: [gmx-users] rerun under non-bonded E. terms

Great! From your last email, I thought there was no way to get what I wanted... I'll read carefully chapter 5! Cheers, Albert On 05/12/2015 02:56 PM, Mark Abraham wrote: Hi, Sorry, actually, that won't help you get non-bonded *forces* since there is no way to decompose them. You can decompo

Re: [gmx-users] rerun under non-bonded E. terms

Hi, Sorry, actually, that won't help you get non-bonded *forces* since there is no way to decompose them. You can decompose energies that way. To get the forces you want, you need a .tpr that has only non-bonded interactions, and to do that correctly, you will have to explicitly list the [exclusio

Re: [gmx-users] rerun under non-bonded E. terms

Thanks to you all, feel free to mark that question as "solved". Best, Albert On 05/12/2015 02:23 PM, Mark Abraham wrote: Hi, Use the nonbonded terms in the .edr files, not the totals. Mark On Tue, May 12, 2015 at 2:32 PM Albert Solernou wrote: Hi Mark, thanks for that. This was the rout

Re: [gmx-users] rerun under non-bonded E. terms

Hi, Use the nonbonded terms in the .edr files, not the totals. Mark On Tue, May 12, 2015 at 2:32 PM Albert Solernou wrote: > Hi Mark, > thanks for that. This was the route that I was taking so far. However, > and I may be missing something, I don't see how your approach excludes > the bonded t

Re: [gmx-users] rerun under non-bonded E. terms

Hi Mark, thanks for that. This was the route that I was taking so far. However, and I may be missing something, I don't see how your approach excludes the bonded terms from the -rerun calculation. Thanks, Albert On 05/12/2015 01:16 PM, Mark Abraham wrote: Hi, This is one of the things for w

Re: [gmx-users] rerun under non-bonded E. terms

Hi, This is one of the things for which mdrun -rerun on a subset trajectory is useful. Make the subset trajectory, make the subset topology (including keeping bonds plus their associated exclusions, as appropriate) and you'll get the forces. tpbconv can make subsets, but YMMV. Mark On Tue, May 1

Re: [gmx-users] rerun under non-bonded E. terms

Hi, I may have not expressed well my final goal. I need a trajectory, a .trr file, that has the forces. I am interested in the non-bonded forces of a sub-set of the residues, so I need to re-compute these, and cannot use the values that come from the full trajectory where all the residues are

Re: [gmx-users] rerun under non-bonded E. terms

On 5/12/15 7:57 AM, Albert Solernou wrote: Thanks Justin, still I would not know how to go from a .edr file into a trajectory that has the forces of the atoms I am interested in. You don't. The .edr file is the energy output of a simulation. If you have your subtrajectory of interest, you

Re: [gmx-users] rerun under non-bonded E. terms

Thanks Justin, still I would not know how to go from a .edr file into a trajectory that has the forces of the atoms I am interested in. Best, Albert On 05/12/2015 12:48 PM, Justin Lemkul wrote: On 5/12/15 7:46 AM, Albert Solernou wrote: Well, back to the beginning, then. Is there a way t

Re: [gmx-users] rerun under non-bonded E. terms

On 5/12/15 7:46 AM, Albert Solernou wrote: Well, back to the beginning, then. Is there a way to do a re-run using only non-bonded energy terms? I'll explain a bit further. I have a trajectory, and want to get a (sub)trajectory that has only a sub-set of atoms and that accounts only for the non

Re: [gmx-users] rerun under non-bonded E. terms

Well, back to the beginning, then. Is there a way to do a re-run using only non-bonded energy terms? I'll explain a bit further. I have a trajectory, and want to get a (sub)trajectory that has only a sub-set of atoms and that accounts only for the non-bonded interactions within this sub-set of

Re: [gmx-users] rerun under non-bonded E. terms

On 5/12/15 6:58 AM, Albert Solernou wrote: Hi, I am getting fairly large values for the LJ energy term (order 10^8), while previous values were much better (order 10^5). I am wondering whether there is a radius decrease for bonded atoms or something equivalent to explain these differences. I br

Re: [gmx-users] rerun under non-bonded E. terms

Hi, I am getting fairly large values for the LJ energy term (order 10^8), while previous values were much better (order 10^5). I am wondering whether there is a radius decrease for bonded atoms or something equivalent to explain these differences. I browsed quickly the manual but could not fin

Re: [gmx-users] rerun under non-bonded E. terms

Thanks for being so quick. Cheers, Albert On 05/08/2015 03:44 PM, Justin Lemkul wrote: On 5/8/15 10:43 AM, Albert Solernou wrote: Thanks Justin, by removing all the bonded terms from the topology you mean edit "topol_Protein_chain_A.itp" and remove the sections "bonds", "pairs", "angles", an

Re: [gmx-users] rerun under non-bonded E. terms

On 5/8/15 10:43 AM, Albert Solernou wrote: Thanks Justin, by removing all the bonded terms from the topology you mean edit "topol_Protein_chain_A.itp" and remove the sections "bonds", "pairs", "angles", and "dihedrals"? Yes, but of course this renders the topology nonfunctional, so make sur

Re: [gmx-users] rerun under non-bonded E. terms

Thanks Justin, by removing all the bonded terms from the topology you mean edit "topol_Protein_chain_A.itp" and remove the sections "bonds", "pairs", "angles", and "dihedrals"? Cheers, Albert On 05/08/2015 03:35 PM, Justin Lemkul wrote: On 5/8/15 10:25 AM, Albert Solernou wrote: Hi All, i

Re: [gmx-users] rerun under non-bonded E. terms

On 5/8/15 10:25 AM, Albert Solernou wrote: Hi All, is there a way to do a re-run using only non-bonded energy terms? Remove all bonded terms from the topology, re-create a .tpr, and re-run. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirsc

[gmx-users] rerun under non-bonded E. terms

Hi All, is there a way to do a re-run using only non-bonded energy terms? Cheers, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Gromacs Users mailing list * Pl