[gmx-users] CompEL bulk offset parameter unavailable in gromacs 5.1.4?
dear all, I am employing the computational electrophysiology scheme in gromacs 5.1.4. I want to set a bulk-offset parameter, such that the scheme only does position exchanges in a region that is remotely enough from my protein. However, it seems that I am not able to set the 'bulk-offset' parameter in any way. Literature review/companion websites however suggest that it is possible, but my mdout-file suggests that the option simply isn't there. Could anyone give me clearance on this? The protocol currently swaps ions close to the proteins that extend out of my nanopore, and it seems to make my simulation unstable. best regards, Henry de Vries -- Henry de Vries Student Topmaster Nanoscience Micromechanics of Materials Group tel: +31 (0)6-30520328 office: X5113.0129 Nijenborgh 4, 9747AG Groningen, Netherlands -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Order in which gromacs calculates non-bonded parameters
Dear all, I was wondering: what priority does GROMACS use for comparing [nonbond_params], [pairtypes], and gen-pairs-based cross-terms? I.e., are pairtypes additive to gen-pairs, with nonbond_params overwriting any cross-term defined through cross-terms? The reason I am asking is that I am currently using tabulated potentials with gen-pairs = no, but I noticed that adjusting cross-terms defined through [pairtypes] does very little to my simulated properties, whereas doing the exact same thing under [nonbond_params] does seem to significantly alter outcomes (i.e. the desired effect). I read the documentation, but am still slightly confused. thank you for reading! Would be great to hear from someone. best regards, Henry de Vries -- Henry de Vries Student Topmaster Nanoscience Micromechanics of Materials Group tel: +31 (0)6-30520328 office: X5113.0129 Nijenborgh 4, 9747AG Groningen, Netherlands -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Computational electrophysiology, implicit solvent and coarse-grained system: atom/molecule definitions?
Dear all, I am currently trying to run the computational electrophysiology scheme on an implicit solvent, coarse-grained system by introducing a little workaround: In the manual, it is stated that we can tell the routine what molecules are 'solvent', and what molecules are 'ions' through custom index groups. As my system thus does not have water molecules, I inserted non-interacting dummy particles into the system, which I then tell the CompEl scheme to use as a solvent group for swapping (via custom index groups) However, the simulation gets stuck at: SWAP: Making sure each atom belongs to at most one of the swap groups. SWAP: Checking whether all ion molecules consist of 20012 atoms SWAP: Checking whether all solvent molecules consist of 20012 atoms SWAP: Opening output file swapions.xvg SWAP: Determining initial ion counts. Looking at swapions.xvg, I see that the routine doesn't recognize my coarse-grained atoms correctly: 4800,7206 and 800 are the correct numbers of coarse-grained atoms that I put in, with 20012 being the total number of coarse-grained beads that I have in my system: # ion group contains 4800 atoms with 20012 atoms in each molecule. # split0 group contains 7206 atoms. # split1 group contains 7206 atoms. # solvent group contains 800 atoms with 20012 atoms in each molecule. Can anyone give me a pointer as to what might be going wrong (I can send the files directly if requested)? Could this be an issue with the coarse-grained model im employing, that it is not defined properly in my topology, or is CompEl really incompatible with any implicit solvent CG-representation that tries to use dummy particles for swapping purposes? Thank you kindly, Henry de Vries -- Henry de Vries Student Topmaster Nanoscience Micromechanics of Materials Group tel: +31 (0)6-30520328 office: X5113.0129 Nijenborgh 4, 9747AG Groningen, Netherlands -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Calculating osmotic coefficient through virial/kinetic terms: what is the handy way?
Dear all, I am trying to find the osmotic coefficient of a set of ions in an implicit solvent system in gromacs 4.5.3. I have found multiple papers reporting an expression of the form: Osm. coefficient = 1- (Virial/Ekinetic). I can find in the manual (appendix B) how the single sum virial is computed (incl. PBC), but I don't completely understand how to extract the virial energy of my system out of my simulation data. g_energy only seems to return vir-XX to vir-ZZ terms, which indicate the tensor components. Is there a handy option that I'm missing that computes the complete virial term of my system, or do I have to manually sum all components? best, Henry de Vries -- Henry de Vries Student Topmaster Nanoscience ZIAM // University of Groningen, NL -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Computational Electrophysiology: how about implicit solvent?
Dear all, In the newest versions of GROMACS the computational electrophysiology method (CompEL) is implemented through the swapping of solvent molecules with ions, thus providing a constant transmembrane potential. However, I am currently employing an implicit solvent model. My question therefore is; is there still a way to implement this charge imbalance protocol if there are no solvent molecules present? - The answer might of course be a no-brainer(read: 'no'), but I was wondering whether there is a workaround for this. Thanks for your time! Best, Henry de Vries -- Henry de Vries Student Topmaster Nanoscience, ZIAM, Rijksuniversiteit Groningen office: X5113.0129 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
