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.war...@pharm.monash.edu.au
Subject: RE: [gmx-users] large number of molecules
To: gmx-users@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.war...@pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
From:
gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@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
Hello,
I
simulate carbon nanotube and basically I follow up
http://cs86.com/CNSE/SWNT.htm
But
when I increase the number of molecules (like 15000) , it gives me wrong
results.
Do
you know why this is happen?
Thank
you,
Kasim
Your
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