Dear Gromacs users,
I am simulating a system containing Protein-Mg-GDP and Protein-Mg-GTP using Gromacs. I have already carried out classical MD simulation for the Protein-Mg-GDP complex. Then, I replaced GDP with GTP in the complex and now have to analyse the structural changes in the Protein-Mg-GTP complex during the simulation. I tried to perform classical MD simulation for the Protein-Mg-GTP complex too. But, as GDP to GTP state transition is a millisecond time-scale event, through classical MD, it seems practically impossible to achieve this time-scale transition. I already have the crystal structure available with me for the Protein-Mg-GTP complex. As, I am new to gromacs, can anybody suggest me any method to perform this transition using some accelerated molecular dynamics method available with gromacs and how it can be performed for my system? Any help will be highly appreciated. Thanks in advance ----- Neeru Sharma, Pune (India)
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