[gmx-users] All-bonds vs h-bonds contraints
Hello Could you please clarify what is the reason for adopting the all-bonds constraints as a standard practice in gmx protein simulations? I mean, the argument that the time step in molecular simulations can be increased by a factor of 4 by replacing the bond vibrations by holonomic constraints' (LINCS paper) seems valid to me in the case of bonds that contain hydrogen (10 fs vibration period for a C-H bond). Why there is a need (if any) to turn ALL bonds to constraints? Furthermore, has anybody seen a difference in the ps/ns protein dynamics when switching from all-bonds to h-bonds constraints? My opinion is that if bond vibrations take place in the fs timescale AND are uncoupled to the slower degrees of freedom , the choice of constraints shouldn't matter, apart from the computation cost of course. I would really appreciate any comments on these issues. Many thanks in advance. George Patargias -- 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] h-bonds constraints for DPPC sim?
Hi It was mentioned here http://lists.gromacs.org/pipermail/gmx-users/2011-May/061475.html that the constraints option may have to be set to h-bonds to get the exp APL in DPPC equilibration/simulation. Is this indeed true and if so how important is it for membrane/protein simulations? Thanks in advance. George -- 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] PRODRG charges
Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get GROMOS-compatible charges? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case that these experimental data are not available for the ligand one is interested in, are DFT/ESP charges acceptable? Thanks again. George g...@bioacademy.gr wrote: Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? Yes, those charges are a reasonable start, but will almost certainly not be sufficient for the final topology. In this case, do we treat all ligand atoms as one charge group? Unless your ligand is 4 atoms or less, no. Please consult the manual regarding charge groups, and see existing Gromos96 building blocks for suitable charge groupings. -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
[gmx-users] PRODRG charges
Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? In this case, do we treat all ligand atoms as one charge group? Thanks. George -- 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
