[gmx-users] questions on distance restraints

[NG HUI WEN]

Dear gmxusers,

I have some questions about distance restraints that I hope you would be able to shed some light on. Thanks in advance.

I am trying to apply distance restraints to my protein. Below was what I did:


-use genrestr to create my ca_disre.itp
genrestr -f membedded_em.gro -o ca_disre.itp -disre (pop-up prompt: CA atoms selected)

-in my mdp file
I added this line near the top:
define          = -DDISRES

-my  top file looks like that
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"

;Include Protein Topology
#include "A2a.itp"

; Include Position restraint file
#ifdef DISRES
#include "ca_disre.itp"
#endif
;
#ifdef POSRES
#include "posre.itp"
#endif
;

;Include POPC topology
#include "popc.itp"
#ifdef LIPID_POSRES
#include "lipid_posre.itp"
#endif

;Include water topology
#include "gromos53a6_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 topology for ions
#include "gromos53a6_lipid.ff/ions.itp"

[ system ]
; Name
Protein and POPC and Water

[ molecules ]
; Compound        #mols
Protein_chain_X     1
POPC              327
SOL         24767
CL          11

The simulation ran without a problem. However, after it was completed, I compared the final protein structure with the initial and it looked like the atoms (even the CA atoms , especially those in the loops) had moved quite a fair bit away from the original position. This made me wonder if the distance restraints had indeed been applied or perhaps the force constant was not large enough (default =1000 kJ/mol/nm^2)?  I had checked the mdout.mdp file "define  = -DDISRES" was there... wasn't sure how else I could check this.

To test whether it was due to the latter, I had tried rerunning the simulation for 1ns simulation with "disre_fc        = 10000" added to the mdp file. This time the atoms did not move as far away as previously observed.

I have tried google-ing for the proper way to impose distance restraints but didn't find my searches too useful. I wonder if anyone could confirm with me that the above method is correct/ tell me that I had done something wrong.

Cheers for that!

Best wishes,
Huiwen



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