Thanks Berk, everything is fine at last. I guess this is my last question : if for example I change three bond lengths from b0A=0.1 to b0B=0.15, when I use gmxcheck with -ab, it prints only one difference between state A and B, instead of 3. Is this ok ?
Maik, what is the power you are using for soft core ? Many thanks Berk and Maik, you greatly helped me.
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