[gmx-users] large number of molecules

[Oliver Stueker]

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