-np is not about number of processors in the case of genion. It's the
number of positive ions to insert.
shaya...@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" <priyankapanwa...@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 <jalem...@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 <
mitomas...@gmail.com <mailto:mitomas...@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 <priyankapanwa...@gmail.com
<mailto:priyankapanwa...@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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