[gmx-users] Help for running gromacs

[priyanka panwar]

Command line was " genion -s em.tpr -o ions.pdb -np 4"

On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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> --
> ========================================
>
> 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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