AMBER Archive (2006)

Subject: AMBER: Non-periodic simulations: How is the system kept together?

Date: Thu Apr 20 2006 - 11:13:04 CDT

Hi all!

I was wondering how non-periodic simulations (ntb=0) work and whether there is
some potential to keep a system together and avoid solvent molecules to drift
off (which I have not seen in my trials..).

If one were to start with an octahedric box, would there be anything to keep it
octahedric during the simulation?

Last, and not very related, is there any input file keyword to determine a
cutoff on the calculation of van-der-waals interactions?

Thank you very much in advance!


Pascal Baillod (PhD student)
Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry
Room BCH 4121, Avenue Forel,
CH-1015 Lausanne
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to