[gmx-users] questions on distance restraints
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Wed Jan 18 01:30:08 CET 2012
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 Protein Topology
; Include Position restraint file
;Include POPC topology
;Include water topology
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include topology for ions
[ system ]
Protein and POPC and Water
[ molecules ]
; Compound #mols
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!
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