Dear gmx users and developers, I am facing a problem that is new for me and I will appreciate advice from your expertise. I am working with a big protein complex (around 100K atoms, several subunits) and I used g_membed to embed it in a (aprox 24 14 nm) pre-equilibrated POPC membrane, however after embedding and a 1ns of NVT equilibration I tried to proced to the NPT equilibration, but I found my system exploding (things moving to fast), so I tried several methods that came to my mind (like decrease the P-coupling constant, decrease the timestep and some others). After few tries I went back to the NVT equilibration and took a look to the pressure, for my surprise I found it to be around 1e30! So I ended with a very compressed system on X-Y, I guess given the embedding of the protein in the membrane. Here are the questions:
1) Are there any reasonable simple method to reduce the pressure on the protein/lipid system? 2) May I expect a very long time to reach the adequate pressure and equilibrium given a possible change on the phase of the lipids by the high pressure? 3) Any other useful direction? Extra information: On this step I had frozen the Protein and excluded the Protein-Protein energy. Thanks, Daniel Silva
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