Thanks Jason for the reply...
I have one doubt here....after the 1st run was complete, the "real" RC
value was 49.60516 while the "target" was 50.65900. So what should be the
value of r2 for setting up the second run starting from previous restart
file.
On Mon, May 11, 2015 at 6:14 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, May 11, 2015 at 2:31 AM, Asmita Gupta <asmita4des.gmail.com>
> wrote:
>
> > Dear users,
> >
> >
> > Is it fine to break a long SMD run into shorter runs? i.e. If i need to
> > extend the distance between two atoms from 28 Ang to 150 Ang, can it be
> > done by extending first from 28 to 50 in 1st run; 50 to 72 in 2nd run and
> > so on...( i am keeping the amount of extension and nstlim same for each
> > run, so that velocity remains constant)?
> >
>
> Yes, this should be fine.
>
>
> > I noticed that when i restart SMD simulation from previous run, the
> > dist_vs_t file generated for each run, shows a sudden drop in force and
> > work values.. something like this:-
> >
> > -------------------------
> > tail dist_vs_t_1st_run
> >
> > 50.65898 49.57840 6.48350 41.66170
> > 50.65899 49.59062 6.41020 41.66177
> > 50.65900 49.60516 6.32301 41.66184
> >
> > -------------------------
> >
> > head dist_vs_t_2nd_run
> >
> > 49.60516 49.62175 -0.09953 0.00000
> > 49.60517 49.63818 -0.19805 -0.00000
> > 49.60518 49.65316 -0.28789 -0.00000
> >
>
> The second column, which is the *real* value of the reaction coordinate,
> *does* appear continuous to me. What does not appear continuous, however,
> is the target value, which goes from 50.659 A to 49.605 A in seemingly 1
> step, while within a segment of the simulation, the distance is changing
> very little. This is why your force is so discontinuous. The values in
> the first column are ones that are derived from your input, so I would
> suggest looking into the source of this RC jump to see if you can pin down
> what's happening (for instance, if the first run didn't complete
> successfully, then the SMD simulation didn't make it all the way to the
> end-point and the second simulation would introduce a discontinuous
> "jump").
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue May 12 2015 - 05:00:04 PDT
