[gmx-users] problem about Pr.mdp

[Justin A. Lemkul]

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

> Thanks Mr.Mark for your reply,
> I am not getting any error, but after Position restrain step, when I see the
> structure of *pr_protein_popc_out.gro in VMD the POPC tails are tilting
> towards backwards(like pulling). It looks there is gap inbetween two
> membrane layers, middle part of the protein appears without covering POPC
> moledules, but water and protein structure are fine.
> Can you pls tell where is the problem ? Is there in any mistake in my *
> pr.mdp file
> I am gving description about what steps i have done:
> 1.The protein simulated in solution for 500ps .
> 2. Protein inserted into POPC by using "genbox".
> 3. Steepest gradient energy minimisation for "protein embedded in POPC
> system"  , here strucure is fine
> 4. Postion restrain for same system
>  - For Protein, POPC and Water force constant -10000 I have used.
>
> I am mentioning my *pr.mdp file
> title               =   popc restrained
> define              =  -DPOSRES  -DPOSRES_LIPID  -DPOSRES_WATER

Try just restraining the protein, otherwise I don't suspect you're accomplishing
much by restraining every component of your system!  That's probably not the
problem, however.  See below.

> 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 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              =  berendsen
> pcoupltype          =  anisotropic
> tau_p                  =     1.0      1.0     1.0     1.0     1.0     1.0
> compressibility     =  4.5e-5   4.5e-5  4.5e-5    0       0       0
> ref_p                  =    1.0      1.0     1.0        1.0       1.0
> 1.0

If I remember the usage of anisotropic pressure coupling correctly, this might
be the source of your problem.  You are applying 1.0 bar of pressure in the
diagonal directions, which I'm guessing is the source of the distortion.    Try
ref_p = 1.0 1.0 1.0 0 0 0

-Justin

> ; Energy monitoring
> energygrps          =  POPC  Protein  SOL_Cl
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  310
> 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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