From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Wed Feb 13 2019 - 16:20:33 CST
Yes. When NAMD restarts and launches ORCA again (assuming you kept the same
qmBaseDir path **and contents*)*, ORCA will use the temporary files left
behind in the folder to start the following steps.
--- Marcelo Cardoso dos Reis Melo, PhD Postdoctoral Research Associate Luthey-Schulten Group University of Illinois at Urbana-Champaign crdsdsr2_at_illinois.edu +1 (217) 244-5983 On Wed, 13 Feb 2019 at 14:47, Francesco Pietra <chiendarret_at_gmail.com> wrote: > Hi > >> For QM/MM simulations to be properly managed by NAMD, your QM >> calculation needs to "fit" inside MD steps. > > > If this is the case, if I understand, by adding > > bincoordinates ./....restart.coor > binvelocities ./.....restart.vel > extendedSystem ./....restart.xsc > > to NAMD config file, and restarting, ORCA takes the checkpoint from folder > "/0". Or not? > > thanks > francesco pietra > > On Wed, Feb 13, 2019 at 7:32 PM Marcelo C. R. Melo <melomcr_at_gmail.com> > wrote: > >> Hi, >> NAMD does not control ORCA in terms of pausing and resuming an SCF >> calculation, so there is nothing in NAMD's config or restart file that >> would inform ORCA of where it sopped, and how should it resume. >> NAMD QM/MM can only be paused/resumed between MD steps, which is were you >> will have "restart" files written. (In your case, given your "restartfreq", >> every 100 MD steps). For QM/MM simulations to be properly managed by NAMD, >> your QM calculation needs to "fit" inside MD steps. >> Best, >> Marcelo >> --- >> Marcelo Cardoso dos Reis Melo, PhD >> Postdoctoral Research Associate >> Luthey-Schulten Group >> University of Illinois at Urbana-Champaign >> crdsdsr2_at_illinois.edu >> +1 (217) 244-5983 >> >> >> On Wed, 13 Feb 2019 at 09:34, Francesco Pietra <chiendarret_at_gmail.com> >> wrote: >> >>> Hello >>> How can NAMD-ORCA QM-MM simulations be correctly restarted? I mean in >>> the context of namd.config in Example1 tutorial: >>> >>> structure XXX_A1_box_ion.psf >>>> coordinates XXX_A1_box_ion.pdb >>>> >>>> # Output Parameters >>>> binaryoutput no >>>> outputname XXX_A1_out >>>> outputenergies 1 >>>> outputtiming 1 >>>> outputpressure 1 >>>> binaryrestart yes >>>> dcdfile XXX_A1_out.dcd >>>> dcdfreq 1 >>>> XSTFreq 1 >>>> restartfreq 100 >>>> restartname XXX_A1_out.restart >>> >>> >>> In particular when no SCF convergence was not yet reached (in favorable >>> cases, info says that SCF convergence is close to be reached), so that >>> XXX_A1_out.restart was not provided. >>> >>> I was also unable to find on ORCA manual how to increase the number of >>> SFC iterations above the default 125. >>> >>> Thanks for advice >>> francesco pietra >>> PS I understand that the ORCA calculation can be carried out separately >>> but I have some reasons now to let NAM-ORCA working together. >>> >>
This archive was generated by hypermail 2.1.6 : Thu Sep 19 2019 - 23:20:17 CDT