Hi all,
I am working on a MD simulation of a membrane protein inside the POPC bilayer using namd. At first, I ran a short constrained dynamics by applying harmonic constraints to both protein and water molecules while keeping the lipid head groups fixed. Then, in another short dynamics run, I relaxed lipids and waters using TCL forces. But, in the first figure you can see the existence of voids between water and bilayer segments which exist for some frames initially and are gone in later frames which is shown in another figure.
My issue is, is my system still correct or not and how can I solve the problem of finding gaps between segments? What can I do to remove these gaps from the beginning ?
Thanks
I'm not sure how you do this in NAMD, but how have you set up your pressure tensors? In gromacs, if you apply pressure on the x, y, z separately (isotropic) you will get voids in bilayers. You'll need to ensure you have semiisotropic pressure coupling applied i.e,. x,z pressure is applied the same, then z (normal to the bilayer) is a separate pressure tensor.
For me it looks just like there was some space between the periodic images of your system at the start of the simulation which later vanished due to NPT conditions, imho nothing to worry about.
Sorry, Roshan, I didn't read your message correctly. If the voids are no longer present than there isn't a problem in the later simulations. I would now suggest calculating lipids area and bilayer thickness to ensure your POPC bilayer is behaving as expected. Also, consider monitoring the box volume during the simulation to see whether the unit cell is fluctuating. The box volume (or unit cell volume) should become stable.
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