On 2/3/15 2:16 PM, Stephen P. Molnar wrote:
Ok. I understand the replys.
I only have a couple of further questions.
A link to grompp is in /usr/local/gromacs/bin.
Why isn't ions.mdp in the run directory and then, where is it?
You download it from the tutorial site.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/04_ions.html
"An example .mdp file (the one we will use) can be downloaded here." The word
"here" is a clickable link to download the file.
-Justin
Thanks in advance.
On 02/02/2015 12:29 PM, HANNIBAL LECTER wrote:
It just means you either missed grompp "-f ions.mdp" ...
OR
the ions.mdp file is not there in the directory where you are performing
your simulations.
On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar <s.mol...@sbcglobal.net>
wrote:
I have installed v-5.0.4 in Debian Wheezy without any warning or erroe
messages.
I have tried running the Lysozyme in Water Tutorial ( the one written for
v-5) and have generated an error message in Step 4.
The message is:
File input/output error:
ions.mdp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I checked the reference and did not find one [defaults] directive in the
.itp file, let alone two
Pleas advise.
Thanks in advance.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and Multivariate
www.FoundationForChemistry.com
(614)312-7528(c)
Skype: smolnar1
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