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
http://ambermd.org/namd/namd_amber.html). 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
AMBER?
~Thomas
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Nov 13 2013 - 07:30:18 PST
