[gmx-users] Continuation = yes keyword

Dawid das addiw7 at googlemail.com
Wed Aug 7 14:26:44 CEST 2019


Thank you Justin.

Best wishes,
Dawid Grabarek

śr., 7 sie 2019 o 13:06 Justin Lemkul <jalemkul at vt.edu> napisał(a):

>
>
> On 8/5/19 10:08 PM, Bratin Kumar Das wrote:
> > Hi,
> > In MD simulation the initial velocity is generated by the Maxwell
> > distribution..Therefore in nvt equilibration we generate the velocity by
> > keeping gen-vel= yes. In the next equilibration step or production md
> step
> > the generated velocity is read by .cpt file. Therefore if we do
> > continuation = no ...along with gen-vel=no ...It may give error
> > message...Otherwise if we use continuation=no...Along with
> gen-vel=yes...It
> > will produce new velocity...Which won't be a continuous simulation..
>
> Beyond compatibility of keywords, the "continuation" setting affects
> constraints. If you say "no," then mdrun will constrain the
> configuration it is supplied, assuming that no constraints have yet been
> solved since it is a new run. If the coordinates supplied are from a
> previous simulation with constraints, then you are likely going to
> change them slightly, thus introducing a discontinuity.
>
> -Justin
>
> > On Tue 6 Aug, 2019, 4:01 AM Dawid das, <addiw7 at googlemail.com> wrote:
> >
> >> Dear All,
> >>
> >> I start my MD simulation from a previous run using data in tpr and cpt
> >> files
> >> with changed mdp options for the new simulation.
> >> Is it really important to use "continuation = yes" for the lincs
> >> constraints.
> >> What can be wrong if I don't (I use continuation = no).
> >>
> >> Best wishes,
> >> Dawid Grabarek
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