I will download latest version of gromacs and start working with it.I will be back if any face any problem. Thanks to all<br><br><div class="gmail_quote">On Mon, May 3, 2010 at 6:39 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
What compilers did you use to install Gromacs? Often times hangs and other memory errors are related to buggy compilers.<br>
<br>
-Justin<br>
<br>
priyanka panwar wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Command line was " genion -s em.tpr -o ions.pdb -np 4"<br>
<br></div><div class="im">
On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
priyanka panwar wrote:<br>
<br>
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>
<br>
That's not a command line. What command did you actually type<br>
(exactly) to run genion?<br>
<br>
<br>
-Group selected was: 12 (SOL)<br>
-Gromacs version I am using is 3.3.1<br>
<br>
<br>
In the absence of any compelling reason (i.e., consistency with<br>
previous simulations), using a Gromacs version that is four years<br>
old is not recommended. The new 4.0.x series is substantially<br>
faster and has many new features.<br>
<br>
-Justin<br>
<br>
On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk<br>
<<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>><br></div><div class="im">
<mailto:<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<br>
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></div>
<mailto:<a href="mailto:priyankapanwar20@gmail.com" target="_blank">priyankapanwar20@gmail.com</a><div class="im"><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<br>
generated<br>
most of the files but unable to generate the ions.pdb<br>
file.The<br>
system is becoming idle after the Selection command. A<br>
line on<br>
the command prompt appears as "replacing solvent molecule<br>
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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-- ========================================<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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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</div></blockquote><div><div></div><div class="h5">
<br>
-- <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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