[gmx-users] Abnormal popc struture after inserting protein

[Justin A. Lemkul]

minnale wrote:
>
>
>   So I dont boughter about those sentences because I confirmed in list 
> archives that I can proceed further steps and moreover em.gro file is  
>     fine, so I went for restrain, here I am getting abnormal POPC 
> structure
> means POPC tails are tilting, water molecules structure also disturbed.
>
> Could you please tell me where iam doing mistake?
>

Not really.  You haven't told us much.  What parameters are you using 
(for the protein and the lipids)?  How did you insert your protein?

Also realize that 50 ps is *extremely* short in the realm of membrane 
protein MD.  Even after several hundred picoseconds things may look a 
bit strange.  Prevailing wisdom is that between 25-30 ns of MD are 
required for the lipids to reach equilibrium (although they should look 
reasonable after just a few ns, but parameters like area per headgroup 
may not level off for a while).

-Justin

> my pr.mdp filetitle              =  protein in popc restrained
> define              =  -DPOSRES_protein
> constraints        =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  10000    ; total 50 ps.
> nstcomm            =  1
> nstxout            =  50
> nstvout            =  1000
> nstfout            =  0
> nstlog              =  10
> nstenergy          =  10
> nstlist            =  10
> ns_type            =  grid
> rlist              =  0.9
> coulombtype        =  PME
> rcoulomb            =  0.9
> rvdw                =  1.4
> pbc                =  xyz
> ; Berendsen temperature coupling is on in three groups
> Tcoupl              =  Berendsen
> tc-grps            =  POPC    Protein  SOL_CL-
> tau_t              =  0.1      0.1      0.1
> ref_t              =  310      310      310
> ; Anisotropic pressure coupling is now on
> Pcoupl              =  berendsen
> pcoupltype          =  anisotropic
> tau_p              =  1.0      1.0    1.0    0        0      0
> compressibility    =  4.5e-5  4.5e-5  4.5e-5  0        0      0
> ref_p              =  1.0      1.0    1.0    0        0      0
> ; Energy monitoring
> energygrps          =  POPC  Protein  SOL_CL-
> ; Generate velocites is on at 300 K.
> gen_vel            =  yes
> gen_temp            =  310.0
> gen_seed            =  173529
>
> Thanks in advance.                       
>
>
>
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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