getting temperature fluctuations of +/- 7 K during the heating and
equilibration of my protein using implicit solvent using AMBER ff14SBonlysc
with igb = 8.
I have approx 1300 atoms in my system.
On 30 June 2018 at 01:03, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> What do you need help doing? The instantaneous temperature will not be a
> fixed value.
>
> On Fri, Jun 29, 2018, 3:30 PM Chhaya Singh <chhayasingh014.gmail.com>
> wrote:
>
> > after the equilibration step. I am doing the MD run.
> > In that, I am getting temperature fluctuations of +/- 5 K .please help
> with
> > this.
> >
> >
> > On 29 June 2018 at 00:12, Chhaya Singh <chhayasingh014.gmail.com> wrote:
> >
> > > After the equilibriation also.. i got the same fluctuations in
> > > temperature.
> > >
> > > On Fri, Jun 29, 2018, 12:10 AM David A Case <david.case.rutgers.edu>
> > > wrote:
> > >
> > >> On Thu, Jun 28, 2018, Chhaya Singh wrote:
> > >> >
> > >> > Thank you for the information.it provided be a clear idea about the
> > >> issue
> > >> > that I was facing.
> > >> > So now I have 1300 atoms in my system but during equilibration, I am
> > >> facing
> > >> > a lot, temperature fluctuations of +/- 7-8 K.
> > >> > How to fix this. Can you help me with this.
> > >> > myheat.out file contains this :
> > >>
> > >> If this is really a "heating" run, where the temperature goes from
> zero
> > >> to 310K, then one would not expect the standard deviation in
> > >> temperatures to tell you much of anything. You certainly need to
> check
> > >> temperature fluctuations after the equilibration is over.
> > >>
> > >> ....dac
> > >>
> > >>
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Received on Fri Jun 29 2018 - 13:00:05 PDT
