Thanks Ross.
On Tue, Sep 24, 2013 at 9:53 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Yes - when you minimize in section the velocities are lost. The heating
> back to 300K is effectively in the stage termed equilibration. Note the
> initial temp tempi=0.0 and the target temperature temp0=300.0. Note the
> simulation here is Alanine dipeptide which is very small so one can be
> quite aggressive when it comes to section 2 and heating things up again.
> Plus the density etc was already equilibrated in the previous step so it
> is not critical to split out heating and equilibration as one would
> normally. However, for a larger system, or to just be more conservative it
> would probably be a good idea to heat things up again slowly for each of
> the different angles.
>
> Hope that helps.
>
> All the best
> Ross
>
> On 9/23/13 8:49 PM, "Sourav Purohit" <sour000.gmail.com> wrote:
>
> >So do you mean that in the tutorial, when minimization is done with
> >dihedral restrained at 120 deg, the velocity information is lost? If so,
> >should we not heat the syatem again ?
> >
> >
> >On Tue, Sep 24, 2013 at 9:06 AM, Ross Walker <ross.rosswalker.co.uk>
> >wrote:
> >
> >> Minimization is simply optimization of coordinates on the potential
> >>energy
> >> surface such that the overall potential energy is reduced. There is no
> >> integration step and thus no concept of temperature.
> >>
> >>
> >> On 9/23/13 8:03 PM, "Sourav Purohit" <sour000.gmail.com> wrote:
> >>
> >> >Hi all,
> >> >
> >> > In AMBER ADVANCED TUTORIAL 17 on finding PMF using Umbrella
> >>Sampling,
> >> >The system has been first minimized, then heated to 300K and then
> >> >equilibriated. Then, after setting the restraint on the dihedral to a
> >> >value
> >> >of 120 deg, the system has been minimized and then equilibriated. I
> >>had a
> >> >doubt on what keeps the temperature maintained at 300K during the
> >> >minimization step.
> >> >Thanks.
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> >>
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Received on Tue Sep 24 2013 - 08:30:03 PDT
