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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
