[gmx-users] large number of molecules

[Justin A. Lemkul]

ksm tprk wrote:
> And one more thing.
> I change morse = no to yes but it was not good too. Do you know why 
> morse does not work?
> 

The "morse" option corresponds to a Morse bond potential, which may or may not 
be appropriate for use with whatever force field you're using (which you haven't 
said).  Haphazardly changing options hoping something works is a good way to 
waste time :)

See my previous mail for other comments.

-Justin

> 
> 
>  > Date: Mon, 8 Mar 2010 18:11:28 -0500
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] large number of molecules
>  >
>  >
>  >
>  > 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
>  > >
>  > >
>  > >
>  > > 
> ------------------------------------------------------------------------
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>  > > 
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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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-- 
========================================

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

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