Thank you Justin, I added rlistlong = 1.4 but still grompp complains: NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.
Why doesn't grompp looks for rlistlong value? Francesco 2013/2/26 Justin Lemkul <[email protected]> > > > On 2/26/13 11:30 AM, francesco oteri wrote: > >> Dear gromacs users, >> in Bjelkmar et al. (2010) where the implementation of CHARMM in GROMACS is >> described, >> the authors say that: >> >> "Electrostatics was treated with particle-mesh Ewald (PME), using a >> short-range cutoff of >> 1.2 nm, and van der Waals interactions were switched off between 1.0 to >> 1.2 >> nm." >> >> I translated this protocol in the following line in mdp file: >> >> ; Neighborsearching >> rlist = 1.2 ; short-range neighborlist cutoff (in nm) >> >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> rcoulomb = 1.2 ; short-range electrostatic cutoff (in >> nm) >> ;VdW >> vdwtype = Switch >> rvdw = 1.2 ; short-range van der Waals cutoff >> (in >> nm) >> rvdw_switch = 1.0 >> >> But grompp complains: >> NOTE 1 [file 02md.mdp]: >> For energy conservation with switch/shift potentials, rlist should be >> 0.1 >> to 0.3 nm larger than rvdw. >> >> >> If I enlarge rlist to 1.3, grompp genrates an error: >> ERROR 1 [file 02md.mdp]: >> With coulombtype = PME, rcoulomb must be equal to rlist >> If you want optimal energy conservation or exact integration use >> PME-Switch >> >> >> So, how can the protocol described in the paper has been implemented? >> >> > Leave rlist at 1.2 and set rlistlong accordingly. The manual description > of rlistlong describes this situation. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
