[gmx-users] Fwd: I have a symmetric simulation box,
jalemkul at vt.edu
Thu Oct 18 12:28:40 CEST 2012
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).
>> 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.
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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
> erikm at xray.bmc.uu.se
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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