[gmx-users] polymer & peptide interaction pbc, visualization problem

[Sezai-Raif Baydan]

Hello!

 

I am trying to simulate the adsorption of a certain peptide on a certain polymer surface. For that, I did position restrain of polymer heavy atom and position restrain of protein heavy atoms during the NVT and NPT equilibration and also during energy minimization (EM). 

 

The first lines of my minim.mdp file looks like this: 

 

; minim.mdp - used as input into grompp to generate em.tpr
define                =  -DPOSRES -DPP_POSRES
integrator    = steep        ; Algorithm (steep = steepest descent minimization)
constraints         =  none

 

The first lines of nvt.mdp and npt.mdp looks like this:

 

define        = -DPOSRES -DPP_POSRES    ; position restrain the protein and polymer 
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 100000        ; 2 * 50000 = 200 ps
dt            = 0.002        ; 1 fs

 

After the equilibration  steps, I run my sytem for 100 ns. In my md.mdp file I just include the position restrain of polymer heavy atoms. 

I also include the position restrain files (posre.itp and posre_polym.itp) in my topology file: 

   

; Include polymer  topology
#include "amber99sb-ildn.ff/polymer_GMX.itp"

; Include Position restraint file for polymer
#ifdef PP_POSRES
#include "posre_polym.itp"
#endif

; Include water topology
#include "./amber99sb-ildn.ff/spce.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 "./amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
peptide and polymer in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Mth                     225
SOL                  8621
CL                        13

 

I do not get any gmx errors! I remove the pbc with: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc -mol -center 

 

When I first upload my md_0_1.gro file in VMD I can see often “artefacts”. So, a monatomic perpendicular fraction of my layer is over my peptide. And that means of course out of the box. But also in some .gro files, I can see a whole monatomic layer over the peptide! Anyway they disappear once I include my noPBC.xtc file. 

 

Once I load my noPBC.xtc file, I saw that the layer is not “stable”. Because when I act out the frames, I see that the layer is shifting over my peptide. It is not the whole layer which is shifting and it is not all the time but in many frames one can see these shifts. I would like to show you some screenshots about this, but the data is too big of one screenshot. 

 

I also try this invocation: trjconv -s md.tpr -f md.xtc -o md_noPBC_whole.xtc -pbc whole -center -ur compact 
                                           trjconv -s md.tpr -f md_noPBC_whole -center -pbc mol 

 

But even then, I have the same problem as described before. 

 

When I use this: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc -mol -ur compact

 

I do not see any shifting of my layer. But this time I cannot see any interactions of my peptide with the layer. 

 

Can somebody help me with this issue? How can I remove the pbc so I do not have any artefacts of my layer so I can see a adsorption of my peptide?