Dear Gromacs Users!<br><br>I have problems during npt equilibration of my solvent box with the CCl4 solvent (I'm preparing this hydrophobic layer for further membrane-mimicking system).<br><br><br>As the result I want to obtain density value ~ 1.5 for such box but between 2 and 3 ns ( where the desity was 1.3) of such simulation I've obtain error<br>
<br>One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.<br><br>1) What should I do in that case ? Should I use larger cutoofs ( I'm using 0.9 nm with the Gromos 56 parameters ) or extend some box vectors ?<br>
<br>2) Initially I've tried to use membrane mimicking dimensions 8.6 6.5 3.0 but during equilibration my box was shrinked to the 8.0 6.0 2.0<br><br>How I could present such shrinking ?<br><br><br>James<br><br><br>