Hello all, I am pulling a 17 amino acid peptide under constraint pulling. Some details:
v = 0.01 nm/ps dt = 0.002 ps steps = 250000 total time = 500 ps My question is: When generating the water box for the simulation, I understand that the edge of the box should be greater than half the cutoff distance. But because the peptide will be stretched a distance of 5 nm by the end of the simulation, is it necessary that the peptide be placed in a box that is > 5nm from the edge of the box? If my cutoff distance is 1.5 nm, will 0.8 nm be sufficient. i.e., which of the below code would be appropriate. I AM using periodic boundary conditions. editconf -f E_min_protein.gro -o E_min_protein_box.gro -bt cubic -d 5.50 or editconf -f E_min_protein.gro -o E_min_protein_box.gro -bt cubic -d 0.80 I have tried both scenarios. The only problem I have is that if the protein is placed in a water box whose edge is placed 5.5 nm from the protein, the simulation takes almost 3 days and 60 Gb. Any tips on reducing the information in the output file? Any help is appreciated. ______________________________ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering "You must be the change you wish to see in the world." --Mohandas Karamchand Gandhi
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