ACtually ,i want to simulate a protein with different types of solvent present like Glycerol+urea+chloride. I created a box with these mix solvents. Now , i am facing the problem is that : how can i place my protein (center of box ) in the mix solvents box. please help me..
thanks in advance !
Justin Lemkul thanks for your response , but i want to know ,how to insert my protein in box center, which already fully filled with mix-solvents??
Solvate with gmx solvate -cs, just like any other solvent box.
However, that approach has the drawback that you have no control over which species get deleted, thus perturbing the concentrations of the co-solvents. My approach has no such problem. You define exactly how many of each species are to be in the box.
for begin it is necessary that you fill your box one by one and at the beginning of filling begins to put the protein and then this how allows you center in the box and after you can put the other mixture in the box: voila this command for center the protein:
gmx_d editconf -center
Sometimes we add - c or -center but still that doesn't bring the protein into the center of the box. In such situation we should check that we are using the right box for the type of protein we are going to simulate.
Details of the various boxes for Gromacs is available at! http://www.strodel.info/index_files/lecture/html/si_boxtypes.html
Good luck
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