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: [email protected]
> To: [email protected]
> 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: [email protected]
> > Subject: RE: [gmx-users] large number of molecules
> > To: [email protected]
> >
> > 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
> > [email protected]
> > +61 3 9903 9167
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to
resemble
> > a nail.
> >
> >
> >
> > *From:* [email protected]
> > [mailto:[email protected]] *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
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