Dear Gromacs Users! 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).
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 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. 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 ? 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 How I could present such shrinking ? James
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