ksm tprk wrote:
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:
Partial information is useless. Post the whole .mdp file; there are plenty of
parameters that can be set incorrectly or inconsistently.
-Justin
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.0005
nsteps = 10000000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Angular
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-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
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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