[gmx-users] large number of molecules

[Justin A. Lemkul]

I wonder what's going on here:

; Groups to couple separately
tc-grps                  = T1 T2 T3 T4 T5 T6 T7
; Time constant (ps) and reference temperature (K)
tau_t                    = 40 0 0 0 0 0 0 40
ref_t                    = 320 0 0 0 0 0 280

So you have multiple parts of your system at different temperatures?  Five 
groups are not coupled, and two are at different temperatures?  Are these 
separate molecules, or different parts of the same CNT?

If they're separate molecules, then angular COM motion removal is inappropriate 
for a periodic system.  Either way, if you have different temperatures for 
different parts of a system, you're likely to get weird, non-physical results.

You will likely have to provide more details on what your objectives are for 
such a setup.

-Justin

ksm tprk wrote:
> I attached my mdp file.
> 
> 
>  > 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

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