27 jul 2007 kl. 10.44 skrev Alif M Latif:
Dear GROMACS Community,
I'm having problem adding spc water molecules into my system
containing lipids molecules totaling 64 of them. My simulation box
size is 1000 nm^3. I told genbox to fill the simulation box with
100 nm^3 of spc216 water molecules using option (-box 4.642 4.642
4.642) due to the experimental formulation of the mixture.
unfortunately, when i view the system, the 100nm^3 of spc216 water
that i fill into the box pushed my lipids to each corners of the
simulation box. Should i proceed with the simulation or can
somebody tell me how to avoid this from happening? Because if the
lipids region is at each of the corners, i'm worried about the
hydrophobic effect of the lipid structures which i want to study. I
wanted the system to be in the box, and the molecules are randomly
scattered.
Are you sure they are not connected by the PBC? I really can't see
how genbox would "push" the lipids around.
/Erik
last simulation when i used 100 nm^3 simulation box, the lipid
structures position and movement exceeded the box in 10 ns of MD
simulation.
Suggestions and advices are greatly appreciated;
Thank You,
M. Alif
Universiti Putra Malaysia
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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