On 10/18/12 6:15 AM, Erik Marklund wrote:
18 okt 2012 kl. 12.08 skrev Ali Alizadeh:
Dear All users
1- I have a symmetric simulation box but i can not produce a symmetric
number density result (number density vs. z direction(nm))
My simulation box is orthorhombic. My boundary condition is pbc but i
don't perform any commands before final run for
Preparation of simulation box(related to pbc) and Just, in my input
file(.mdp file) select pbc xyz-option.
1- construction of simulation box with a software
2- pdb2gmx for producing .gro and .top
3- energy minimization
4- nvt(it converged)
5- npt(it converged)
6- production of md(2 nano second)
A simulation length of two nanoseconds is probably too short. The files you
emailed me off-list showed that your density plot was fairly normal, just rough.
Simulate longer, and perhaps discard some of the initial frames as
equilibration (standard practice).
-Justin
2- I don't locate the centre of masses. How can i determine it?Is it necessary?
The center of mass is undefined for a periodic system.
--
Sincerely
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
--
========================================
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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