[gmx-users] large number of molecules
ktoprak2 at hotmail.com
Tue Mar 9 00:03:49 CET 2010
My mdp file is what http://cs86.com/CNSE/SWNT.htm has. I used nose-hoover for Tcouple.and the beginning of mdp code looks like:
; RUN CONTROL PARAMETERSintegrator = md; Start time and timestep in pstinit = 0dt = 0.0005nsteps = 10000000; For exact run continuation or redoing part of a runinit_step = 0; mode for center of mass motion removalcomm-mode = Angular; number of steps for center of mass motion removalnstcomm = 1; group(s) for center of mass motion removalcomm-grps =
I used gromacs 3.3.3 and in the vacuum. I applied the heat first around 10 layers.after I finished my simulation and look at the edr file, the result temperatures are higher than what I gave. It looks like it generates heat by it self.But when I do same simulation with less molecules such as 6000, it looks fine.
Date: Tue, 9 Mar 2010 08:57:12 +1100
From: Dallas.Warren at pharm.monash.edu.au
Subject: RE: [gmx-users] large number of molecules
To: gmx-users at gromacs.org
You are going to have to provide a lot more details than that if
you want some help.
What is “wrong results”? What is your input (copy and paste
some commands in)? What is the output (copy and paste)? What makes you think
the results are “wrong”? In what situations are they “right”? … and there are
a lot more questions that could be asked ……
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences,
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble a
gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On
Behalf Of ksm tprk
Sent: Tuesday, 9 March 2010 8:33 AM
To: gromacs users
Subject: [gmx-users] large number of molecules
simulate carbon nanotube and basically I follow up http://cs86.com/CNSE/SWNT.htm
when I increase the number of molecules (like 15000) , it gives me wrong
you know why this is happen?
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