Hi,<div>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.<br><br><div class="gmail_quote">
On Mon, May 3, 2010 at 6:02 PM, <span dir="ltr"><<a href="mailto:shayamra@post.tau.ac.il">shayamra@post.tau.ac.il</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<br>
No need to include "-np 4" at all. genion command does not take advantage of multiple processors (nor does it need to).<br>
<br>
Try rerunning the command without -np 4.<br>
<br>
-Shay<div><div></div><div class="h5"><br>
<br>
Quoting "priyanka panwar" <<a href="mailto:priyankapanwar20@gmail.com" target="_blank">priyankapanwar20@gmail.com</a>>:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Command line was " genion -s em.tpr -o ions.pdb -np 4"<br>
<br>
On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
priyanka panwar wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
Thanks for help.<br>
-Command line was:<br>
Number of (3-Atomic) solvent molecules:4256<br>
Replacing solvent molecule 499 (atom 2784) with Na<br>
<br>
</blockquote>
<br>
That's not a command line. What command did you actually type (exactly) to<br>
run genion?<br>
<br>
<br>
-Group selected was: 12 (SOL)<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
-Gromacs version I am using is 3.3.1<br>
<br>
<br>
</blockquote>
In the absence of any compelling reason (i.e., consistency with previous<br>
simulations), using a Gromacs version that is four years old is not<br>
recommended. The new 4.0.x series is substantially faster and has many new<br>
features.<br>
<br>
-Justin<br>
<br>
On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk <<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<a href="mailto:mitomaster@gmail.com" target="_blank">mitomaster@gmail.com</a> <mailto:<a href="mailto:mitomaster@gmail.com" target="_blank">mitomaster@gmail.com</a>>> wrote:<br>
<br>
Please post more details including the following:<br>
<br>
* What is the exact command line?<br>
* What group do you select as a "continuous solvent"? I know it<br>
might sound weird to ask this but what I learned while<br>
teaching students is that these questions really should be<br>
asked when there are problems.<br>
* Which version of Gromacs are you using?<br>
<br>
<br>
2010/5/3 priyanka panwar <<a href="mailto:priyankapanwar20@gmail.com" target="_blank">priyankapanwar20@gmail.com</a><br>
<mailto:<a href="mailto:priyankapanwar20@gmail.com" target="_blank">priyankapanwar20@gmail.com</a>>><br>
<br>
<br>
I am using Gromacs for Simulation of Insulin.I have generated<br>
most of the files but unable to generate the ions.pdb file.The<br>
system is becoming idle after the Selection command. A line on<br>
the command prompt appears as "replacing solvent molecule with<br>
Na" and remains as such for many hours. Is this step really<br>
takes too much time or I am doing something wrong. Thanks<br>
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</blockquote>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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