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<div>Hi</div>
<div>From Justin,</div>
<div>"If you say that you have 20 mM<br>of ligand, which corresponds to 18 ligands attached to one protein, why not just<br>put 18 molecules in your unit cell with one protein? " </div>
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<div>=> I want to save the simulaiton time since i will run the simulation up to 1 micro-sencond.</div>
<div>=> 18 ligand + one protein ( 7nm x 7nm x 7nm)</div>
<div>=> 10 ligand + one protein ( 6nm x 6 nm x 6nm)</div>
<div>=> ( 7nm x 7nm x 7nm) is twice size of ( 6nm x 6nm x 6nm)</div>
<div>=> increase four times simulation time </div>
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<div>From Justin,</div>
<div>"can you guarantee that the ligands will interact the same way as if<br>you add ten at a time? Will they aggregate? Will they inherently bind the<br>protein in the same way, or will it be different? "</div>
<div>=> I don't know, but I assume that will make little difference.</div>
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<div>Thank you</div>
<div>Lin</div>
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<div>Chih-Ying Lin wrote:<br>><br>> HI<br>> I am simulating the protein + ligand + water molecules system.<br>> In the experimental work, the concentration of ligand is pretty low, say<br>> under 20 mM (avearge 18 ligands attached on one protein)<br>
> It will be a huge system to create a system with 20 mM and it will take lot<br>> of simulation time.<br>> Instead, I create a 6nm x 6nm x 6nm simulation box and put one protein<br>> molecule with 10 ligands.<br>
> After 100 nano seconds, 10 ligands are attached on the protein.<br>><br>> Then, for this one protein with 10 ligands attached + water molecules<br>> I will do the following steps =><br>> 1. remove the water molecules<br>
> 2. center the protein with 10 ligands attached in the 6nm x 6nm x 6nm<br>> simulation box<br>> 3. put another 10 ligands around the protein with 10 ligand attached<br>> 4. solvate the system<br>> 5. add ions<br>
><br>> Are the above steps make sense to create a low concentration simulation?</div>
<div>Your procedure sounds more like a titration with increasing concentration,<br>rather than modeling a low concentration system. If you say that you have 20 mM<br>of ligand, which corresponds to 18 ligands attached to one protein, why not just<br>
put 18 molecules in your unit cell with one protein? You may never be able to<br>achieve the actual concentration, but you can certainly model the mole ratio.</div>
<div>The other concern would be - if a system initially had 20 ligands (or 18,<br>whatever), can you guarantee that the ligands will interact the same way as if<br>you add ten at a time? Will they aggregate? Will they inherently bind the<br>
protein in the same way, or will it be different?</div>
<div>-Justin</div>
<div>> Thank you<br>> Lin<br>></div>