Dear Justin, Thanks for the wonderful suggestions which is very clear and informative but I am confused about some points below
1. Actually my protein is human mitochondrial protein so I have used GROMOS 96 53a6 ff. is it correct? but you have mentioned about the condition applied, so I don't understand this point because I have a normal protein which bind on the mitochondrial membrane. So according to you which conditions should i applied? which preferences you are talking about? Due to have limited configuration of our hardware we are using core2duo single processor with 4 GB RAM. So dear please suggest me the concise requirements for this simulation. 2. My protein does not depend on the temperature that means it is not thermophilic or mesophilic protein. So for large simulations is it correct to apply REMD technique. I think that ED sampling should be best but don't know which should be taken for reference structure. I have tell you about my system and protein so please suggest me the sampling technique is effective in my protein case. 3. I know about the energy conservation but don't know about the simulation stability. So please also tell me is PCA should be performed for simulation stability or something else analysis should be performed. 4. Why 4-5 fs is more effecient than 3fs? -- Pawan
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