Flat bottomed position restraints not working as intended

User discussions
1

GROMACS version: 2021.5
GROMACS modification: No

Hello I’m trying to simulate a system with 8 identical peptides and a lipidic membrane, but I want the peptides to interact with only one leaftlet of the membrane. I was told to use Flat-Bottomed position restraints to keep the peptides on one side. But it’s not working as intended, I’ve run a test for 200 ns and the peptides appear kinda locked into place. This isn’t what I want I only want the peptides to be restricted to the upper half of the box.

My system can be seem in this picture

npt
npt640×514 188 KB

My topol file can be seen below

#include "./charmm36-jul2022-napht.ff/forcefield.itp"

#include "napht-bp100.itp"
#ifdef POSRES
#include "posre.itp
#endif

;;;Flat bottom position restraints
 [ position_restraints ]
; i funct g r k
   1     2    5   0.5  1000
  19     2    5   8.0  1000
  20     2    5   8.0  1000
  28     2    5   8.0  1000
  30     2    5   8.0  1000
  32     2    5   8.0  1000
  38     2    5   8.0  1000
  40     2    5   8.0  1000   
  42     2    5   8.0  1000
  60     2    5   8.0  1000
  62     2    5   8.0  1000    
  64     2    5   8.0  1000
  82     2    5   8.0  1000
  84     2    5   8.0  1000
  86     2    5   8.0  1000
 101     2    5   8.0  1000
 103     2    5   8.0  1000
 105     2    5   8.0  1000
 121     2    5   8.0  1000
 123     2    5   8.0  1000 
 125     2    5   8.0  1000
 143     2    5   8.0  1000
 145     2    5   8.0  1000
 147     2    5   8.0  1000
 165     2    5   8.0  1000
 167     2    5   8.0  1000
 169     2    5   8.0  1000
 184     2    5   8.0  1000
 186     2    5   8.0  1000
 188     2    5   8.0  1000
 203     2    5   8.0  1000
 205     2    5   8.0  1000
 207     2    5   8.0  1000
 225     2    5   8.0  1000
 227     2    5   8.0  1000  
 229     2    5   8.0  1000
 246     2    5   8.0  1000
 248     2    5   8.0  1000  
   
#include "popg.itp"
; Include Position restraint file
#ifdef POSRES_POPG
#include "posre-popg.itp"
#endif

#include "popc.itp"
; Include Position restraint file
#ifdef POSRES_POPC
#include "posre-popc.itp"
#endif

; Include water topology
#include "./charmm36-jul2022.ff/tip3p.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 "./charmm36-jul2022.ff/ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein           8
POPG             64
POPC             64
SOL         7690
CLA              40
SOD              64

There is not enough information about how to used flat-bottomed postion restraints only, so I used what I could gather from the documentation and posts here on bioexcel.

Any help will be appreciated.

Thanks

2

You restraint setup looks correct to me. Could it be that you have set -DPOSRES in your mdp file, which activates the normal position restraints (as well)?

3

Hi, thank you very much for your reply.

I just checked my mdp file and I didn’t set -DPOSRES.

I’m still unsure what is causing the problem I’m going to try changing the reference positions on the restraints and run it again. Thanks

4

Dear @TGaziri , I’m trying to simulate a system with a drug and membrane, and I want the drug to interact with only the upper leaflet of the membrane. Can I use the flat bottom position restrain? Did you do it for your system?

5

Hi @Elahe. I put this project on standby, I didn’t do it yet, I believe that you can use flat bottomed potential for your drug.