[gmx-users] Justin-lipid tutorials..

[Justin A. Lemkul]

On 5/19/12 7:49 AM, rama david wrote:
> 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 ..
>

If a small void develops during NVT but closes during NPT, there's nothing 
wrong.  It occasionally happens.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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