That depends on what the problem is. It's always best to quote the
exact error message when asking for help :-) If you're referring to the
use of -conc and -neutral, those were not available in version 3.1.
It's always recommended to use the newest version of the software,
unless, for some specific reason, you need to use an old version.
-Justin
[EMAIL PROTECTED] wrote:
Hi Tsjerk,
Thanks for the tutorial. I was going through the steps and ran into a
problem when placing in the ions in order to neutralize the system. Would
this because my version of Gromacs is 3.1 and your tutorial is for v3.3.3?
Thanks for the help,
-John
Hi,
For a tutorial and a workflow you can also check out:
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/01-Preparation-Workflow.jpg
A bit in progress still, and any comments welcome ;)
Cheers,
Tsjerk
On Sat, Jun 21, 2008 at 9:40 AM, Vitaly Chaban <[EMAIL PROTECTED]> wrote:
Special thanks to Vitaly, Mark and Justin for there comments. I've
revisited the wiki site and read through chapter 5 of the manual. I'm
currently going through the tutorial with a standard protein. I run
into a
problem when I use the command:
grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr
The error states that the em.mdp file doesn't exists, but none of the
steps in the tutorial leading up to this command creates the em.mdp
file.
I was just wondering what step in the process is the .mdp file created
or
do I have to have that already created off to the side ready for the
grompp command?
Thanks again,
-John Landers
I guess em.mdp is a parameter file for energy minimization. Look here:
http://www.gromacs.org/documentation/reference/online/mdp.html for how
one can make it. If you want to make an energy minimization of your
system firstly, you just have to change
"integrator = md"
to
"integrator = l_bfgs"
or
"integrator = steep"
I have also sent you personally the ready example to start with
simulating carbon nanotube.
Best,
Vitaly
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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