[gmx-users] T-coupling of water and ion
Anton Feenstra
feenstra at few.vu.nl
Mon May 30 08:25:08 CEST 2005
zouj01 at mails.tsinghua.edu.cn wrote:
> tc-grps = RNA SOL_Na
> tau_t = 0.1 0.1
> ref_t = 400 400
[...]
> # System RNA SOL Na SOL_Na
> 200 269 405 266 504 266
[...]
> tc-grps = RNA SOL Na
> tau_t = 0.1 0.1 0.1
> ref_t = 400 400 400
[...]
> # System RNA SOL Na SOL_Na
> 200 268 248 268 350 268
[...]
I don't understand your results. You couple (in all cases) to 400K,
while your system seems to be about 300K on average. You have
'gen_vel=no', meaning you use starting velocities (if any) from your
input structure file. Where did you get that from?
If you do not couple Na+ separately, and it remains bound to the RNA, it
may not exchange heat enough with the water. This can explain the
relative high T for your Na+ ions (and for the RNA).
> I use different time step and bond option for these 2 tests.
> And I use afm pulling options.
> I'm not sure whether these mdrun options will also influence the T-coupling.
Using 1fs timestep and no constraints vs. 2fs with constraints can
already give different temperature behaviour, mainly due to more or less
(roundoff) errors (which can heat), and the effect of constraints (which
can cool).
--
Groetjes,
Anton
* NOTE: New Phone & Fax numbers (below) *
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
|_____________|_______________________________________________________|
More information about the gromacs.org_gmx-users
mailing list