# How to pull a molecule across the bilayer? **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, pull-code\ **Created:** [August 3, 2021, 2:58pm UTC](https://gromacs.bioexcel.eu/t/how-to-pull-a-molecule-across-the-bilayer/2632 "2021-08-03T14:58:49Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![drrahulsuresh](https://avatars.discourse-cdn.com/v4/letter/d/e68b1a/32.png) [@drrahulsuresh](https://gromacs.bioexcel.eu/u/drrahulsuresh)\ **Post date:** [August 3, 2021, 2:58pm UTC](https://gromacs.bioexcel.eu/t/how-to-pull-a-molecule-across-the-bilayer/2632/1 "2021-08-03T14:58:49Z")
GROMACS version: 2019.4 GROMACS modification: No integrator = md dt = 0.002 nsteps = 5000000 nstxout = 500 nstvout = 500 nstfout = 500 nstcalcenergy = 100 nstenergy = 100 nstlog = 100 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw\_switch = 1.0 rvdw = 1.2 ; tcoupl = Nose-Hoover tc\_grps = SYSTEM tau\_t = 1.0 ref\_t = 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 = SYSTEM ; refcoord\_scaling = com ; Pull code pull = yes pull\_ncoords = 1 ; only one reaction coordinate pull\_ngroups = 2 ; two groups defining one reaction coordinate pull\_group1\_name = lipids pull\_group2\_name = POL pull\_coord1\_type = umbrella ; harmonic potential pull\_coord1\_dim = N N Y ; pull along z pull\_coord1\_groups = 1 2 ; pull\_coord1\_start = yes ; define initial COM distance \> 0 pull-pbc-ref-prev-step-com = yes pull-coord1-geometry = cylinder pull\_coord1\_vec = 0.0 0.0 1.0 pull\_coord1\_rate = 0.0001 ; pull\_coord1\_k = 1000 ; kJ mol^-1 nm^-2 I have already posted this on the forum and still couldn’t resolve the issue. So I am posting it again. The above is my pull code. I am trying to pull a small molecule POL across the bilayer. The molecule seems unaffected by the pull command. The molecule fluctuate in the middle of the bilayer. I have tried various values for k and rate, still no update with result. Could anyone guide me thru this? ---
**Author:** ![Anirban12](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/anirban12/32/495_2.png) [@Anirban12](https://gromacs.bioexcel.eu/u/Anirban12)\ **Post date:** [August 13, 2021, 6:54am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-a-molecule-across-the-bilayer/2632/2 "2021-08-13T06:54:44Z")
Hi @drrahulsuresh, Please see the paper here. > **[Molecular Dynamics Simulations of Membrane–Sugar Interactions](https://pubs.acs.org/doi/10.1021/jp402385d)** > > It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by... I would like to know is POL hydrophilic or hydrophobic? You can change the rate to 0.01 or -0.01 and see if there is any difference. As a beginner I am also struggling to pull a carbohydrate molecule across bilayer. So it would be great to see you solve this issue. Thanks and regards. Anirban ---
**Author:** ![drrahulsuresh](https://avatars.discourse-cdn.com/v4/letter/d/e68b1a/32.png) [@drrahulsuresh](https://gromacs.bioexcel.eu/u/drrahulsuresh)\ **Post date:** [August 13, 2021, 9:03am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-a-molecule-across-the-bilayer/2632/3 "2021-08-13T09:03:48Z")
Hi The molecule is 1,3 butadiene. its hydrophobic. I have already tried with different values of rate. I will try this as well. Thank you @Anirban12 ---
**Author:** ![drrahulsuresh](https://avatars.discourse-cdn.com/v4/letter/d/e68b1a/32.png) [@drrahulsuresh](https://gromacs.bioexcel.eu/u/drrahulsuresh)\ **Post date:** [August 14, 2021, 7:44am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-a-molecule-across-the-bilayer/2632/4 "2021-08-14T07:44:38Z")
If I reduce the rate to 0.01 or -0.01 i end up with error “Distance between pull groups 1 and 2 (4.130297 nm) is larger than 0.49 times the box size (4.130255)” ---
**Author:** ![Anirban12](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/anirban12/32/495_2.png) [@Anirban12](https://gromacs.bioexcel.eu/u/Anirban12)\ **Post date:** [August 14, 2021, 2:36pm UTC](https://gromacs.bioexcel.eu/t/how-to-pull-a-molecule-across-the-bilayer/2632/5 "2021-08-14T14:36:23Z")
Hi @drrahulsuresh The negative rate actually does opposite of what positive rate does [push towards membrane or pull from membrane]. And this particular error is because POL now can see periodic image of the membrane, the distance between groups cannot be more than box/2. Does the position of POL changes now? If it does not, u can try with higher k value like 1500 or 2000. You can also change the geometry from cylinder to distance and check. Hope these will help you. Thanks and Regards Anirban ---
**Author:** ![drrahulsuresh](https://avatars.discourse-cdn.com/v4/letter/d/e68b1a/32.png) [@drrahulsuresh](https://gromacs.bioexcel.eu/u/drrahulsuresh)\ **Post date:** [January 25, 2022, 9:26am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-a-molecule-across-the-bilayer/2632/6 "2022-01-25T09:26:25Z")
Hi. Sorry for very late reply. Gor occupied with other bunch of works. Actually it didn’t work. Still at the same place