[gmx-users] Help for running gromacs

[shayamra at post.tau.ac.il]

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