Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD

From: Thomas Evangelidis <>
Date: Wed, 13 Nov 2013 17:27:15 +0200

Hi Pawel,

> Just o clarify this and your follow up question: I would be worried
> about those gaps. To me it looks like somehow your periodic box does not
> correspond to the box that was used to solvate the molecule. As said
> before, if you'd like to simulate a hexagonal system it's as simple as
> creating a triclinic cell with a a c 90 90 120 cell parameters. In NAMD
> you need to transform that into the cartesian basis and feed those
> values to the cellBasisVector cards.
I did some tests today and found out what Jason pointed out: NAMD ignores
the information in .rst/.inpcrd file (the last line) and uses only the
cellBasisVector1, cellBasisVector2, cellBasisVector3 parameters to form the
unit cell - this must be clarified in Since the initial hexagonal box
has approximately the same dimensions with the hexagonal box dimensions
printed in the .xsc (NAMD extended system file) upon NPT equilibration then
I don't find a reason to worry. If you looked at the equilibration
trajectory (frames between the starting and final states I showed) you
could see that NAMD rotates the hexagonal box with respect to the axis
normal to a-b plane to fill the gaps.

> One other idea: if I understand correctly that system you showed was set
> up with NAMD. Why not set up a hexagonal system with Amber and compare?
> If done correctly they should look the same.
Do you mean setting a,b,c,alpha,beta,gamma to d,d,h,90,90,120, solvating in
LeAP, saving a .prmtop/.inpcrd and then running an NPT equilibration with


Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

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Received on Wed Nov 13 2013 - 07:30:18 PST
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