Re: question on heating

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Apr 18 2007 - 05:29:49 CDT

Hi guys,

Thank you for your comments.

Leandro: the constraints are not "fixed-atom" ones (I'm not a big fan
of "fixing" atoms). Constraints I apply are usually "smooth", so that
at the end I don't get the buggy clashes you mentioned. In general,
I've been using such approach to equilibrate my systems, and it has
worked out very well for me.

I forgot to mention that I'm trying to simulate a protein-membrane
system, so in this case the situation becomes a little bit more
complicated -I rather say "a pain in the neck"-. I'll see what I get
and will write back if further problems appear.

Cheers,
Michel

2007/4/17, Leandro Martínez <leandromartinez98_at_gmail.com>:
>
>
> After heating you should run for a while rescaling the temperature
> to 310K several times, in order that the kinetic energy converges to the
> the one corresponding to 310K. However this difference in
> temperature is not probably causing
> your rattle problem. If you constraint is a "fixed-atom" constraint, you
> should minimize the energy after removing it, because there may
> be large repulsions that are not being computed while you thermalize
> you system. In general you could equilibrate your system to 310K with
> constraints, relieve the constraints, minimize the energy again, and
> then equilibrate to 310K again for a while, thus getting a constraint-free
> equilibrated system.
> Leandro.
>
>
>
>
>
> -------------------------------------------------------------------
> Leandro Martinez
> Institute of Chemistry
> State University of Campinas
> http://www.ime.unicamp.br/~martinez/packmol
> http://www.ime.unicamp.br/~martinez/lovoalign
> --------------------------------------------------------------------
>
>
>
> On 4/17/07, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> > Hi guys,
> >
> > I was wondering if you could help me with this issue. I'm using the following lines within my input file in order to warm up the system:
> >
> > set temp 0;
> > while { $temp < 310 } {
> > langevinTemp $temp
> > run 3000
> > output ssra-heat
> > set temp [expr $temp + 31]
> > }
> >
> > The target temp is 310. However, when I run it like that (assuming increments of 31 K each), the final temp after heating is about 278 K. If I set the value to 30 K, then the final temperature is around 300 K, but it never reaches 310. This small thing is causing me a lot of problems, because after some time (specially when I perform the "zero-constraint" equilibration stage) I always get a complaint from the RATTLE algorithm. Am I missing something?
> >
> > Thanks!
> > Michel
> >
> >
>
>

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