[gmx-users] Help for running gromacs

[Erik Marklund]

-np is not about number of processors in the case of genion. It's the 
number of positive ions to insert.

shayamra at post.tau.ac.il skrev:
> 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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>>
>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/