# Issue of membrane protein with lipid bilayer

**URL:** <https://gromacs.bioexcel.eu/t/issue-of-membrane-protein-with-lipid-bilayer/4810>\
**Category:** User discussions\
**Tags:** mdp-parameters\
**Created:** [September 18, 2022, 3:06am UTC](https://gromacs.bioexcel.eu/t/issue-of-membrane-protein-with-lipid-bilayer/4810 "2022-09-18T03:06:16Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![lei123](https://avatars.discourse-cdn.com/v4/letter/l/cab0a1/32.png) [@lei123](https://gromacs.bioexcel.eu/u/lei123)\
**Post date:** [September 18, 2022, 3:06am UTC](https://gromacs.bioexcel.eu/t/issue-of-membrane-protein-with-lipid-bilayer/4810/1 "2022-09-18T03:06:16Z")

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GROMACS version:4.5  
GROMACS modification: No  
Here post your question  
Hi,  
I am a new user of Gromacs. When I try to do MD of membrane protein with a POPC bilayer. The results are strange. Many lipid molecule were stretched to a straight line in the box. The equilibration results seems right. Below is the mdp parameters, which is from CHARMM GUI prepared files, just changed nsteps. Does anyone know what the problem is. Thanks in advance.

 ![截屏2022-09-18 上午10.47.43](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/04cd4a60b059cb893bf38decddda54eb64749883.jpeg)

integrator = md  
dt = 0.002  
nsteps = 100000000  
nstxout = 50000  
nstvout = 50000  
nstfout = 50000  
nstcalcenergy = 100  
nstenergy = 1000  
nstlog = 1000  
;  
cutoff-scheme = Verlet  
nstlist = 20  
rlist = 1.2  
vdwtype = Cut-off  
vdw-modifier = Force-switch  
rvdw\_switch = 1.0  
rvdw = 1.2  
coulombtype = PME  
rcoulomb = 1.2  
;  
tcoupl = Nose-Hoover  
tc\_grps = SOLU MEMB SOLV  
tau\_t = 1.0 1.0 1.0  
ref\_t = 303.15 303.15 303.15  
;  
pcoupl = Parrinello-Rahman  
pcoupltype = semiisotropic  
tau\_p = 5.0  
compressibility = 4.5e-5 4.5e-5  
ref\_p = 1.0 1.0  
;  
constraints = h-bonds  
constraint\_algorithm = LINCS  
continuation = yes  
;  
nstcomm = 100  
comm\_mode = linear  
comm\_grps = SOLU\_MEMB SOLV

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 18, 2022, 3:51am UTC](https://gromacs.bioexcel.eu/t/issue-of-membrane-protein-with-lipid-bilayer/4810/2 "2022-09-18T03:51:37Z")

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This is a periodicity issue. Use `gmx trjconv` to make molecules whole in the trajectory.

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<div class="post-metadata">

**Author:** ![lei123](https://avatars.discourse-cdn.com/v4/letter/l/cab0a1/32.png) [@lei123](https://gromacs.bioexcel.eu/u/lei123)\
**Post date:** [September 18, 2022, 7:35am UTC](https://gromacs.bioexcel.eu/t/issue-of-membrane-protein-with-lipid-bilayer/4810/3 "2022-09-18T07:35:29Z")

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Thanks for your suggestion. I’ll try to fix it.

Best regards