[gmx-users] Justin-lipid tutorials..
ramadavidgroup at gmail.com
Sat May 19 13:49:36 CEST 2012
Hi Gromacs friends ..
I am doing justin Lipid-tutoria on lipid ..
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 ...!!!
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
1. Use position restrained upto 100000 on lipid phosphate head group in z
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
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,
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