[gmx-users] still problem of pr.mdp

[Justin A. Lemkul]

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi gmxusers,
> i have used below parameters those what you suggested ,
>
> title               =   popc restrained
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  10000    ; total 20 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 two 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              =  parrinello-rahman
> 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
> gen_seed            =  173529
> ~
>
> ~
>
>  but still i am getting "tilting structure of POPC" except water and protein
> stucture( fine) . I am using protein restrain force 1000 and my system box
> size is 7nm.
> Pls help me.......
>

You have not told us what force field you are using to represent your system. 
If you're using the POPC parameters from Tieleman, this would be strange, but
if you're using some random parameters you found somewhere that haven't been
properly validated, the behavior you're seeing might be expected :-)  Also
realize that 20 ps is extremely short when it comes to bilayer equilibration. 
I believe the literature agrees upon at least several nanoseconds (and maybe
upwards of 20-30, depending on who you ask!) to get proper equilibration of
lipids.  I would suggest running a longer simulation (like 1 ns) to see if that
alleviates your problem.

-Justin

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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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