[gmx-users] MD at different temperatures without pressure coupling

[Christoph Freudenberger]

Ester Chiessi wrote:
> Hi Gromacs people,
> 
> I prepared a model of a polymer in SPC water and I used PBC to mantain the
> covalent connectivity of the chain across boundaries.
> I started a MD calculation at 300 K ( Berendsen T coupling) without pressure
> coupling and it seems it's going on.
> 
> I'd like to perform corresponding MD calculations at different temperatures (313
> and 323 K) but without introducing pressure coupling, because I'm afraid it might
> disrupt my periodic connectivity.
> 
> Is it possible?
I think so... I could imagine that it might even work with pressure coupling.
I don't think the box will expand to much... if even at all within this small
range of temperature. Just try ;-)

> When I used genbox to solvate the polymer, was SPC water pre-equilibrated at
> 300 K?

AFAIK if you used genbox -cp polymer -cs -o box or something similar the
water molecules come from $GMXDATA/top/spc216.gro. That is a box equil. at
300K. But I dont think that matter much for you. You have to minimize
and requilibrate your system anyhow. I'd suggest to do a short run at
300K before raising the temperature.

hope that helps
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785