Dear Users,
Sorry for maybe naive question. I am new user of gmx. I like to fix the positions of three atoms in three neighboring residues (not connected) with respect to each other. These atoms are very close to each others and van der waals interaction makes the distance larger after em. However, I like to keep the distance between these atoms constant. I am wondered whether freezed groups is working in energy minimization? Alternatively, I was thinking of excluding the interactions between the heavy atoms on this centers during the em to get the desirable structure. or maybe to increase the force constant on these heavy atoms? I would appreciate any suggestions in the this regard. Best regards, Saman
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