AW: Self-Assemble Monolayer--Periodic Boundary Conditions

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Sep 30 2014 - 01:38:57 CDT

• Next message: Haleh a: "Folic acid parameters"
• Previous message: Niklaus Johner: "Re: PCL dcd files"
• In reply to: Natnael Doilicho: "Self-Assemble Monolayer--Periodic Boundary Conditions"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

So you want to keep cell size in X and Y and only want to adapt pressure in Z?

useflexiblecell yes

useconstantarea yes

Otherwise please explain more general.

Norman Geist.

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Natnael Doilicho
Gesendet: Dienstag, 30. September 2014 01:03
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Self-Assemble Monolayer--Periodic Boundary Conditions

Hi all,

I am simulating an Alkanethiol Self-Assembled Mononlayer.

The layer has at its base a hexagonally patterned plane of Sulfur atoms, each 5 Angstroms from one another.

When I run the equilibration (under NPT conditions), the adjacent image cells move closer to the original, disturbing the 5 Angstrom exclusion distance between the sulfur atoms around the edges of the square system.

Is there a way to limit or cease this universal contraction?

Thanks,

Natnael Doilicho

University of Chicago

---
Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.
http://www.avast.com

• Next message: Haleh a: "Folic acid parameters"
• Previous message: Niklaus Johner: "Re: PCL dcd files"
• In reply to: Natnael Doilicho: "Self-Assemble Monolayer--Periodic Boundary Conditions"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:53 CST