Hi Thomas,
On 11/13/2013 10:27 AM, Thomas Evangelidis wrote:
> 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).
From the referenced webpage: " NAMD will not read the box information
from the crd/rst file generated from tleap/sleap."
> 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?
Yes, that's what I meant but without the NPT equilibration part. All I
meant was if you had doubts about the periodic hexagonal system that
NAMD set up for you, you could set up the same system with AMBER and
compare.
Pawel
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 13 2013 - 08:00:02 PST
