From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Tue Apr 17 2007 - 16:33:05 CDT
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.
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Leandro Martinez
Institute of Chemistry
State University of Campinas
http://www.ime.unicamp.br/~martinez/packmol
http://www.ime.unicamp.br/~martinez/lovoalign
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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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