[gmx-users] Justin-lipid tutorials..
Justin A. Lemkul
jalemkul at vt.edu
Sat May 19 13:53:53 CEST 2012
On 5/19/12 7:49 AM, rama david wrote:
> 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 ..
If a small void develops during NVT but closes during NPT, there's nothing
wrong. It occasionally happens.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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