Dear Gromacs users!
I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found that command like genrestr -f b2ar.gro -disre -index.ndx -o test.itp will produce some distance restricted matrix of the whole groups presented in the index.ndx file. So how I could select to contrain selected residues within selected distance by means the index file? E.g I've manually point out 2 residues in index.ndx. I waant to preserve between that residues some desired distance D wich I've obtaine from the experimental data. How I could do it via genrestr and waht addition flags should I use for that purpose ? 2) Is there any way to apply gradually the desired dist.resrs during MDrun to prevent some artifacts in my system wich would occur due to the rapid application of the dis.res ( e.g in cases where the conformation of the started structure and that wich I'd obtained fter application of the restrains are slightly different)? Thanks for help, James
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