[gmx-users] large number of molecules

[Justin A. Lemkul]

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.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 nail.
> 
>  
> 
> *From:* 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
> 
>  
> 
> 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 E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up 
> now. <http://clk.atdmt.com/GBL/go/201469229/direct/01/>
> 
> 
> ------------------------------------------------------------------------
> Hotmail: Powerful Free email with security by Microsoft. Get it now. 
> <http://clk.atdmt.com/GBL/go/201469230/direct/01/>
> 

-- 
========================================

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

========================================