[gmx-users] Justin-lipid tutorials..

rama david 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 ...!!!
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

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
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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