I am going to start by quoting: Chapter 3 of the Gromacs manual (page 14)<br><br>"length of each box vector must exceed the length of the macromolecule in the direction of that edge plus two times the cutoff radius Rc" Then it states:
<br><br><span style="font-style: italic;">"It is common to compormize in this respect and make the solvant layer somewhat smaller in order to reduce the computational cost"</span><br><br>For a protein aligned along the z-axis in a lipid . The protein length is
5.3 nm and the lipid layer (already equilibraited with solvants) is 6.73 nm. I am using a cubic box.<br><br> I have no problem with the x and y edges which are long to accomodate enough lipid molecules.<br><br>My questions:
<br>1. Protein is closer to one edge than the other. Does this make any difference? <br> The solvants are part of equilibritaed lipid.<br><br>Along protein axis:<br> a. The periodic image is 1.43 nm away. (along protein axis)
<br> b. The distance between the protein and its mirror image is: 0.8 nm on one side and 2.0 nm on the other side? (These affect PME - coulmb interactions). Will these cause trouble?<br><br>2. Is it necessary to keep the protein at least
1.5 nm away from the edges normal to z-axis? This more than doubles the number of solvant molecules. ---- <br><br>I have simulations with less than 50,000 atoms (protein, solvants, and KcsA). But no one realy says much about the box sizes.
<br><br>What is the common practice? Please give examples?<br>and <br>How much compromise is acceptable ? "<span style="font-style: italic;">It is common to compormize in this respect !!!"<br><br>Thanks<br>Mohamed Osman
<br><span style="font-style: italic;"><br>=======================<br></span>Professor of Electrical Engineering<br>Washington State University<br>Pullman, WA 99164-2752<br></span><br>