On 5/15/13 7:36 AM, aixintiankong wrote:
i want to study how ligands change the conformations using the gromacs
software and i want to run 100ns, but i don't konw how to reasonably set the
nstxout nstvout nstenergy nstlog and nstxtcout.
There is no universal answer. The main considerations are disk space and time
scale on which pertinent events occur. grompp will warn you if you are
producing a large amount of data, which makes the disk space problem easy to
assess. As for the time scale of events, you will have to think about the types
of motions you are hoping to see and save accordingly.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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