<p><u><font color="#810081">Dear Gromacs users. I ve been trying to run a MSD for a G coupled receptor and encountered some problems during my run. <br>I have encountered a methodology that deals with this type of transmembrane proteins, and apparently I need to assemble my box with a "tri" layer, water/decane/water. I found an article entitled "A molecular Dynamics Study of the Decane/water interface", where the author studies several aspects in the usage of such boxes.<br>
I need help on how to put together all these water molecules and decane molecules in the same box. <br>I thought about simply creating theses boxes in separate using gromacs, and then simply copying and pasting the coordenates of the molecules into the same topology file. Apparently I was too naive to think that this simplistic approach would actually work.<br>
Thank you in advance </font></u><a href="mailto:gmx-users@gromacs.org"></a></p>