[gmx-users] Help for running gromacs

[Justin A. Lemkul]

priyanka panwar wrote:
> Hi,
> Thanks for help.
> -Command line was:
> Number of (3-Atomic) solvent molecules:4256
> Replacing solvent molecule 499 (atom 2784) with Na

That's not a command line.  What command did you actually type (exactly) to run 
genion?

> -Group selected was: 12 (SOL)
> -Gromacs version I am using is 3.3.1
> 

In the absence of any compelling reason (i.e., consistency with previous 
simulations), using a Gromacs version that is four years old is not recommended. 
  The new 4.0.x series is substantially faster and has many new features.

-Justin

> On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk 
> <mitomaster at gmail.com <mailto:mitomaster at gmail.com>> wrote:
> 
>     Please post more details including the following:
> 
>         * What is the exact command line?
>         * What group do you select as a "continuous solvent"? I know it
>           might sound weird to ask this but what I learned while
>           teaching students is that these questions really should be
>           asked when there are problems.
>         * Which version of Gromacs are you using?
> 
> 
>     2010/5/3 priyanka panwar <priyankapanwar20 at gmail.com
>     <mailto:priyankapanwar20 at gmail.com>>
> 
>         I am  using Gromacs for Simulation of Insulin.I have generated
>         most of the files but unable to generate the ions.pdb file.The
>         system is becoming idle after the Selection command. A line on
>         the command prompt appears as "replacing solvent molecule with
>         Na" and remains as such for many hours. Is this step really
>         takes too much time or I am doing something wrong. 
>         Thanks
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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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