Hi Gromacs friends ..
I am doing justin Lipid-tutoria on lipid .. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html I completed upto the ion addition and energy minimisation.. While doing equilibration I stuck with the following problem .. 1. While NVT I found that protein are moving towards water and two layer are getting separated 2. Running NPT on the lipid separated layers in nvt.gro (get from above nvt ) I found that both layer come to close again ...!!! in NPT So is it right or any wrong happen ??/ To solve the nvt lipid layer separation problem I am using the following way mentioned by Justin advanced trouble shoot page... 1. Use position restrained upto 100000 on lipid phosphate head group in z direction.. IN these case lipid layer still separated by small distance.. 2 I change the vanderwall radii to 0.350 and 0.320 (Tutorial mention to 0.375 ) to add more water .. But in both time at nvt lipid layer get separated Please give me valuable suggestion .. Thank you in advance.. With Best wishes, Rama David
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