[gmx-users] Help for running gromacs

[priyanka panwar]

Hi,
I tried it that way also, but in that case it displays a message "No ions to
add and no potential to generate" and it is also not generating ions.pdb
file but it is creating genion.log file.

On Mon, May 3, 2010 at 6:02 PM, <shayamra at post.tau.ac.il> wrote:

> Hi,
> No need to include "-np 4" at all. genion command does not take advantage
> of multiple processors (nor does it need to).
>
> Try rerunning the command without -np 4.
>
> -Shay
>
>
> Quoting "priyanka panwar" <priyankapanwar20 at gmail.com>:
>
>  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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>>>>
>>>>
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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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>>
>
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