Dear All
I am conducting a MD simulation for membrane protein with GMX 4.0.5. I met
lots of LINCS warnings (almost for angle change of N-H and C-H bond) when
doing equilibration for the membrane-protein system under NPT condition. I
had doing energy minimization (emtol = 500) before the equilibr
li lv wrote:
Dear All
I am conducting a MD simulation for membrane protein with GMX 4.0.5. I
met lots of LINCS warnings (almost for angle change of N-H and C-H bond)
when doing equilibration for the membrane-protein system under NPT
condition. I had doing energy minimization (emtol = 500
Dear Justin
Thanks for your reply. Generally I conduct the simulation following the
tutorial on your website. The system contains an integrin alpha2b/beta3
transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer and
solvated in water. The initial membrane-protein system is built
li lv wrote:
Dear Justin
Thanks for your reply. Generally I conduct the simulation following the
tutorial on your website. The system contains an integrin alpha2b/beta3
transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer
and solvated in water. The initial membrane-pro
Dear Justin
Thanks greatly for your suggestions. I will try a new series of EMs and NPT
equilibrations to find whether it will be of effect.
Li
2011/5/14 Justin A. Lemkul
>
>
> li lv wrote:
>
>> Dear Justin
>>
>>
>> Thanks for your reply. Generally I conduct the simulation following the
>> tu
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