[gmx-users] change of bilayer structure during NVT equilibration

[Justin Lemkul]

On 10/6/13 10:57 AM, shahab shariati wrote:
> Dear Justin
>
> Very thanks for your quick reply.
>
>> Depends on how you prepared the system.
>
> For initial structure of system, I used coordination from website:
> http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html
>

Note that these lipids require different .mdp settings than what you posted, 
which appear to be from my tutorial.  Settings are not generally transferable 
between force fields!  Consult the references provided at that site; the correct 
settings are described in the papers.

>> Probably there were voids in the solvent or lipid headgroups that caused
>> distortion in the system.
>
> When I see the initial structure of system by VMD, There is no voids in the
> solvent or lipid headgroups, apparently.
>

OK, makes sense if you're using a pre-equilibrated structure.

>> Restraints on the lipid headgroups along z could help.
>
> I want use restraints on the dopc and chol molecules (lipid molecules). For this
>
> purpose, I did following:
>
> 1) I used genrestr tool twice. genrestr gave me 2 files (lipidchol.itp and
> lipiddopc.itp for cholesterol and dopc molecules, respectively).
>

genrestr only works for one molecule at a time, as its help information warns. 
The restraint files you get will be junk.

> 2) I added define = -DPOSRES in mdp file.
>
> 3) I added Include Position restraint file to the topology file.
>
> My topology file is as follows:
>
> ; Include forcefield parameters
> #include "gromos-43a1-s3_lipid.ff/forcefield.itp"
>
> #include "cholesterol.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "lipidchol.itp"
> #endif
>
> #include "dopc.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "lipiddopc.itp"
> #endif
>
> #include "gromos-43a1-s3_lipid.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> #include "gromos-43a1-s3_lipid.ff/ions.itp"
>
> [ system ]
> ; Name
> dopc/chol/sol
>
> [ molecules ]
> ; Compound        #mols
> CHOL        26
> DOPC       102
> SOL       1706
> --------------------------------------------------------------------------------
> When I used grompp, I encountered error:
>
> Fatal error:
> [ file lipidchol.itp, line 34 ]:
> Atom index (30) in position_restraints out of bounds (1-29).
> This probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
> ---------------------------------------------------------------------------------
> How to fix this issue?
>

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

Restraining the entire lipid is counterproductive as it inhibits equilibration. 
  My suggestion was to restrain the headgroups, or maybe even better, just one 
atom (like P) along the z-axis.  Doing so allows freedom of motion in the x-y 
plane but prevents serious distortion along z.  You can write the .itp files for 
these by hand.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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