[gmx-users] T-coupling of water and ion
spoel at xray.bmc.uu.se
Sat May 28 09:25:35 CEST 2005
On Sat, 2005-05-28 at 12:41 +0800, zouj01 at mails.tsinghua.edu.cn wrote:
> Hi all,
> I post this question to the list several days ago. but do not receive any response
> by now. Therefore let me put it again.
> I am interested in how to set the T-coupling group.
> for system containing Protein(or nucleic acid), water, and ions(eg. Na), many
> people do T-coupling seperately with water and ion, ie. Protein SOL ION.
> While others put water and ion in one tc_group, ie. Protein SOL_ION.
> What's the difference between these two tc_grps selections?
> Do they influence much the simulation results?
Very slightly because when combining the groups you rely on correct
exchange of heat between solvent and ions, which is not given. You
shouldn't combine non-polar and polar groups in one (or protein and
water). You can test it with a short simulation and look at the average
temperature and the fluctuations of each group (if you save velocities
you can still compute the T using g_traj).
> Does the latter save some simulation time?
> If I only care the behavior of the biomolecule, could I use the latter for my
> tc_group setting?
> Thank you very much for your comment.
> Jian Zou
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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