[gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Christopher Neale chris.neale at alum.utoronto.ca
Tue Apr 21 13:10:20 CEST 2015

Dear Mahender:

It's a real pity that the pull_geometry = position has been removed. So now it's impossible to do umbrella sampling of a solute across a lipid bilayer properly? Anyway, I see a note about this removal here ( http://redmine.gromacs.org/issues/1346 ), though no reason is given. I'd suggest that you revert to a more functional version of gromacs ;)

Hopefully I'm missing something and somebody else can point you to a better solution.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of mahender singh <pharmbiochem at live.com>
Sent: 20 April 2015 05:27
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Dear Gromacs users

I am trying to pull a drug molecule across the plasma membrane, from one side to the another side of the membrane. But when I am using pull_geometry= position, it's giving error, as I found that this option is removed in the gromacs 5.0.4. So I am using pull_geometry  = distance, but with this option I am able to pull the drug upto center of the membrane, because COM distance between the pull group and the reference group will become zero and beyond this point drug will not move. I am using following parameters for the pull code

; Pull code
pull        = umbrella
pull_geometry    = distance
pull_dim    = N N Y
pull_start    = yes
pull_ngroups    =2
pull-ncoords    =1
pull_coord1_groups    = 1 2
pull_group1_name    = NPROT_ref
pull_group2_name    = LIG
pull_coord1_rate    = -0.0020        ; 0.0020 nm per ps = 2 nm per ns
pull_coord1_k        = 1000        ; kJ mol^-1 nm^-2
pull_nstxout    = 500        ; every 1 ps
pull_nstfout    = 500        ; every 1 ps

group1 is the lipid membrane and LIG is the drug molecule (drug molecule is placed in the lower leaflet of the membrane and center of the membrane is at Z=0).
 Can anyone kindly suggest me what could be the solution, if I need to pull the drug across the membrane or Am I making some mistake in understanding the pull code parameters?
Also the force in the pullf.xvg is on the negative side, what I understood from that the force is in negative sign because there is decrease in the COM of the pull and reference group during the smd simulation, am I correct?

thanks in advance, for any help, comments or suggestions.

with regards
Mahender singh

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