Hi Justin: Thanks for your reply. Yes, I did everything you mentioned. Let me explain my steps in a bit more detail.
1) I had a lipid bilayer and a peptide from a previous simulation (in a box 15 nm x 7.5 nm x 7.5 nm- 15 nm being perpendicular to the plane of the bilayer). I removed the water and the peptides, so I had only the bilayer left. 2) I then resized the box using editconf (the -box option) to a cubical box of 7.5 nm in all directions. The bilayer remained in the center of the new box. 3) I then re-inserted the peptide by editing the coordinate file, and ran an energy minimization. Then I added water using genbox, and ran another EM. 4) Then I ran the simulation for 3,000,000 steps (90 ns). While this was happening, I observed that the size of the box was beginning to change, in the z direction (not in the y direction as I said yesterday, but still, parallel to the plane of the bilayer). I've included some pictures here (in the .tga format), from before and after the simulation. When I ran it in vmd using the initial coordinates and the trajectory file, I could actually see the box resizing during the run. https://www.dropbox.com/l/UJuFbDTPaISIpkSf I'm sure there's a very simple explanation, but I can't seem to figure it out. Thanks! Regards, Bharath On 2/6/13 11:52 AM, Bharath K. Srikanth wrote: > Hi everyone, > Today, I was attempting a simulation of a system with a lipid bilayer, and > the size of my simulation box, obtained from a previous simulation, was 15 > nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane > of the bilayer). The bilayer consisted of 128 DOPC lipids and was located > at the centre of the box. I used periodic boundary conditions in all three > directions. > I then resized the box to 7.5 nm in all directions, using the editconf -box option. After doing the requisite energy minimization steps, I ran the simulation using mdrun. However, running the simulation caused the box > to gradually shrink in the y-direction (parallel to the plane of the bilayer!) during the simulation, ultimately settling at around half the original dimension. Is there anything I may have done that could cause this effect? I'm thoroughly baffled. What do you mean by "resized the box?" Did you strip out water, adjust box vectors, re-solvate, equilibrate, etc? What you're describing is very weird; pictures, plots, etc would help a lot here. -Justin -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
