Hi,
The problem is the temperature at which the heating up ends is 300K. So the
next step should start at 300K and because I have used a heat bath, should
ideally stick around 300K. But what happens is that the next step
(equilibration) starts at 200K and keeps on increasing which is very
unusual. I want to have a distance dependent dielectric of epsilon=r. That
is why I have dielc=1 and eedmeth=5 . If there is any other way to do it I
would like to know.
Thank you
Sajeewa
On Fri, Jun 1, 2012 at 9:47 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Jun 01, 2012, Sajeewa Pemasinghe wrote:
> >
> > After heating my system up to 300K with the mdin.2 input file (shown
> below)
> > I am trying to equilibrate my system at 300K (gradually removing
> > constraints) using mdin.3 input file (shown below). Instead of starting
> at
> > 300K and proceeding at 300K the simulation starts at a temperature of
> 200K
> > and increases temperature at every step.
>
> You mdin.3 file sets irest=1, which will start the simulation at the same
> temperature as the last one ended. Check that comparison. As per my usual
> advice: when you have problems, run a short simulation with ntpr=1 to see
> more
> about what is going on.
>
> We don't recommend using ntt=1 for implicit solvent simulations; ntt=3 will
> give you much better temperature regulation.
>
> FWIW, we don't recommend using eedmeth=5 either. Please be *sure* that is
> what you really want to do.
>
> ....dac
>
>
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Received on Fri Jun 01 2012 - 08:00:03 PDT
