[gmx-users] large number of molecules

ksm tprk ktoprak2 at hotmail.com
Tue Mar 9 19:08:43 CET 2010 

Yes I was using ffgmx. I tried to use oplsaa but it didn't work. I am using gromacs 3.3.1 and it looks like it doesn't have n2t file beside ffgmx.How can i use oplsaa in gromacs 3.3.1


> Date: Mon, 8 Mar 2010 18:34:23 -0500
> Subject: Re: [gmx-users] large number of molecules
> From: ostueker at gmail.com
> To: jalemkul at vt.edu; gmx-users at gromacs.org
> CC: 
> 
> Hi Karim,
> 
> On Mon, Mar 8, 2010 at 18:11, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > 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.
> 
> In addition to Justin, you haven't told us even which forcefield you are using.
> I hope it's not ffgmx as it is in the reference you gave us. Search
> the Archive and the Gromacs wiki for reasons not to use ffgmx.
> 
> Oliver
> 
> > -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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> >
> > --
> > ========================================
> >
> > 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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> 
> 
> 
> -- 
> Oliver Stueker
> Post-doctoral Fellow, Bader Lab
> Donnelly CCBR, University of Toronto, Canada
> http://baderlab.org
> phone: +1 (416) 978-0571
> -- 
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