# Position restraint problem

**URL:** <https://gromacs.bioexcel.eu/t/position-restraint-problem/12460>\
**Category:** User discussions\
**Created:** [July 30, 2025, 8:48am UTC](https://gromacs.bioexcel.eu/t/position-restraint-problem/12460 "2025-07-30T08:48:43Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![erolic](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/erolic/32/2053_2.png) [@erolic](https://gromacs.bioexcel.eu/u/erolic)\
**Post date:** [July 30, 2025, 8:48am UTC](https://gromacs.bioexcel.eu/t/position-restraint-problem/12460/1 "2025-07-30T08:48:43Z")

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GROMACS version: 2024.2  
GROMACS modification: No  
I am trying to simulate protein-ligand complex, where ligand was parameterized using acpype. When I check with gmx dump command and visualize the trajectory I see that ligand is not restrained during equilibrium simulations. I am providing the topol\_new.top, and posre\_UNK\_itp.log below.

the mdp file that I use shown below;

title = Protein-ligand complex NVT equilibration  
define = -DPOSRES ; position restrain the protein and ligand  
; Run parameters  
integrator = md ; leap-frog integrator  
nsteps = 500000 ; 2 \* 500000 = 1000 ps  
dt = 0.002 ; 2 fs  
; Output control  
nstenergy = 5000 ; save energies every 10.0 ps  
nstlog = 5000 ; update log file every 10.0 ps  
nstxout-compressed = 5000 ; save coordinates every 10.0 ps  
; Bond parameters  
continuation = no ; first dynamics run  
constraint\_algorithm = lincs ; holonomic constraints  
constraints = h-bonds ; bonds to H are constrained  
lincs\_iter = 1 ; accuracy of LINCS  
lincs\_order = 4 ; also related to accuracy  
; Neighbor searching and vdW  
cutoff-scheme = Verlet  
ns\_type = grid ; search neighboring grid cells  
nstlist = 20 ; largely irrelevant with Verlet  
rlist = 1.2  
vdwtype = cutoff  
vdw-modifier = force-switch  
rvdw-switch = 1.0  
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)  
; Electrostatics  
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics  
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)  
pme\_order = 4 ; cubic interpolation  
fourierspacing = 0.16 ; grid spacing for FFT  
; Temperature coupling  
tcoupl = V-rescale ; modified Berendsen thermostat  
tc-grps = Protein\_UNK Water\_and\_ions ; two coupling groups - more accurate  
tau\_t = 0.1 0.1 ; time constant, in ps  
ref\_t = 310 310 ; reference temperature, one for each group, in K  
; Pressure coupling  
pcoupl = no ; no pressure coupling in NVT  
; Periodic boundary conditions  
pbc = xyz ; 3-D PBC  
; Dispersion correction is not used for proteins with the C36 additive FF  
DispCorr = no  
; Velocity generation  
gen\_vel = yes ; assign velocities from Maxwell distribution  
gen\_temp = 310 ; temperature for Maxwell distribution  
gen\_seed = -1 ; generate a random seed

[topol\_new.top](https://gromacs.bioexcel.eu/uploads/short-url/meeThTtNPnx1hVmuwN9oUoSBidD.top) (1.0 MB)  
[posre\_UNK\_itp.log](https://gromacs.bioexcel.eu/uploads/short-url/dXVM4wEbopXEa3UJvVCVJhssQn4.log) (2.7 KB)

I have check the output of gmx dump -s npt.tpr | grep posres, it is obvious only protein atoms are restrained.  
can anyone help to solve that issue? thanks.

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<div class="post-metadata">

**Author:** ![erolic](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/erolic/32/2053_2.png) [@erolic](https://gromacs.bioexcel.eu/u/erolic)\
**Post date:** [July 30, 2025, 3:47pm UTC](https://gromacs.bioexcel.eu/t/position-restraint-problem/12460/2 "2025-07-30T15:47:10Z")

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solution :

paste [atomtypes] section from UNK.itp, and paste it just after the ;

Include forcefield parameters  
#include “amber99sb.ff/forcefield.itp”

then, remove [atomtypes] from UNK.itp, and save it.