[gmx-users] Technical

pawan raghav pwnrghv at gmail.com
Tue Jun 29 10:10:31 CEST 2010

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?

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