[gmx-users] large number of molecules

ksm tprk 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 ……


Catch ya,

Dr. Dallas Warren

Drug Delivery, Disposition and Dynamics

Monash Institute of Pharmaceutical Sciences,
Monash University

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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