Hello!
When i did the steered Molecular Dynamics using the method of LCOD, i want to study the effect of waters on the system and i added several waters which were closing the binding site into QM region. To avoid the crash of the calculation, i added very weak restraint on these waters. But someone told me that it was unpossible to use restraint on the steered MD. According to my final result, the plot of reaction coordinates vs handle possition was not linear, instead, all of points were at the two extremities and it was the same for the curve of work vs reaction coordinates. I really dont know how to explain it....
So what should i do in this case if i want to know the effect of waters ? I couldnt do the adaptive MD because of the version of amber. Thanks very much for your any suggestion.
Best regards
Kexin CUI
23/10/2015
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Received on Fri Oct 23 2015 - 02:30:04 PDT
