[gmx-users] Single long simulation versus multiple short ones

[Tsjerk Wassenaar]

Hey Widya,

In general, no, 15*2ns is not equal to 1*30ns. The reason for this lies in
correlation and relaxation times. 15 simulations of 2ns give good statistics
on relaxation and, if the system is equilibrated already, on short-term
processes. A single simulation of 30 ns may relax to equilibrium, where a
too short simulation does not and may show long term processes that extend
2ns. Yet a single simulation is only a single observation, such that the
statistics are rather poor.

Hope it helps,

Tsjerk

On Jul 25, 2011 4:56 PM, "Widya Desmarani" <widya.desmarani at gmail.com>
wrote:

Dear gromacs user,

I have been trying to look for an answer for my following question from our
forum but still couldn't manage to find one. Probably it is trivial but I am
not sure.

Instead of running a single relatively long simulation (say for about 30
ns), is it acceptable if we simulate multiple short simulations (say 15
simulations where each of them is 2 ns), and then, all the resulted
trajectories are merged/concatenated into one single trajectory with the
amount of total simulation 30 ns? I am interested in investigating bulk
properties of liquid, such as compressibility, diffusion, and dielectric.

Many thanks.

Regards,
Widya

--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110725/5db11b39/attachment.html>