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I'm a gromacs noob, so I appreciate your patience. I tried simulating the interaction of a protein with 100 copies of the same ligand, in water. The workflow I used is attached here as a picture. The simulation did weird things, specifically: the ligands all appear to have connections, and the protein contorted severely during the simulation. Can anyone point me in the direction of simple fixes? protein contortionligands inappropriately connected

    gmx pdb2gmx -f pro.pdb -o pro.processed.gro
    gmx insert-molecules -ci jz4.gro -nmol 100 -box 10 10 10 -o jz4.box.gro
    gmx solvate -cp jz4.box.gro -cs spc216.gro -p jz4.top -o jz4_solv.gro
    gmx editconf -f pro.gro -o final.gro -box 10 10 10 -center 5 5 5
    gmx solvate -cp final.gro -cs jz4_solv.gro -o final.box.gro -p topol.top

Add jz4.prm to topol, like this:

; Included forcefield parameters
#include "./charmm36-jul2022.ff/forcefield.itp"

#include "jz4.prm"

Added jz4.itp to position restraints, like this:

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

#include "jz4.itp"

    gmx grompp -f ions.mdp -c final.box.gro -p topol.top -o ions.tpr
    gmx genion -s ions.tpr -o final.box.gro -p topol.top -pname NA -nname CL -neutral
Selected SOL

    gmx grompp -f em.mdp -c final.box.gro -p topol.top -o em.tpr
    gmx mdrun -v -deffnm em
    gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
    gmx mdrun -deffnm nvt -v
    
Changed barostat to c-rescale

    gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
    gmx mdrun -deffnm md_0_1 -nb gpu
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  • $\begingroup$ +1 but an you please paste into a code block and remove the screenshot? $\endgroup$ Mar 30, 2023 at 23:54
  • $\begingroup$ @NikeDattani thanks, fixed. $\endgroup$
    – hbc8
    Mar 31, 2023 at 0:01
  • $\begingroup$ Thanks. For future reference, please see this: mattermodeling.meta.stackexchange.com/q/411/5 $\endgroup$ Mar 31, 2023 at 0:02
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    $\begingroup$ Are you sure GROMACS is the issue? To me, it looks like most of the "weird" bonds are to atoms on the other side of the periodic box (e.g., the atom or molecule moved across the unit cell boundary). In that case, it's the visualization or topology, not the simulation. $\endgroup$ Mar 31, 2023 at 3:20
  • $\begingroup$ @GeoffHutchison Thanks for replying. Yeah I don't claim gromacs is the issue, but I'm not sure where the weird bonds are coming from among the commands I used. I followed JD Tamucci's reply here researchgate.net/post/… $\endgroup$
    – hbc8
    Mar 31, 2023 at 13:25

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