[gmx-users] build membrane system from Charmm-Gui

Xiang Ning xiang_ning at yahoo.com
Sun Aug 24 22:36:21 CEST 2014

Dear Justin,

Thanks for your help! It did work when I use grompp to generate tpr file. However, after obtaining  em.tpr file, I want energy minimization of the membrane+water+ion system, so I typed "mdrun -v -deffnm em", and the outcome em.gro file looks really weird by using VMD to view. The original file is water above the lipid membrane, but now by viewing em.gro, the water is now in the middle of two membrane leaflet, and they aparted to 4 parts! I would like to know what is wrong? Is it because the mdp file? Thanks very much for your assistance!


my mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist         = 1                 ; Frequency to update the neighbor list and long range forces
ns_type         = grid          ; Method to determine neighbor list (simple, grid)
rlist           = 1.2           ; Cut-off for making neighbor list (short range forces)
coulombtype     = PME           ; Treatment of long range electrostatic interactions
rcoulomb        = 1.2           ; Short-range electrostatic cut-off
rvdw            = 1.2           ; Short-range Van der Waals cut-off
pbc                 = xyz               ; Periodic Boundary Conditions

On Friday, August 22, 2014 4:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 8/22/14, 4:36 PM, Xiang Ning wrote:
> Hi All,
> I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with pdb2gmx to get top file (I used charmm36), then I would like to know, how to add water and ions back to the system? I read the previous solution was to modify [molecules] in top file (add ions and waters information manually), are there any detailed explanation of how to do that?

For the coordinates, just paste the water and ion coordinates back into the 
membrane-only file.  For the topology, indeed all you need to do is modify 
[molecules] in the .top to reflect however many waters and ions there are in the 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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