minnu vijayan wrote:
hello friends
for doing normal mode analysis i am trying to create .mtx file .but in
output i am not getting thi .mtx file..what all precautions i have to take
with thanks
To get the attention of someone who deals with normal modes, it would be best to
start a new thread with an appropriate subject line. Joining in on an existing
thread with unrelated content will often get your question overlooked (or ignored).
Now, to attempt to answer your question. There are many things that could be
going wrong, but no one on this list can read your mind or figure out what
exactly you're doing. So here are some tips:
1. Post the text of your .mdp file
2. Show the *exact* command line you're using with mdrun
3. Provide the version of Gromacs you're using, at the very least, to rule out
old versions and fixed bugs. Information about your system and how Gromacs was
compiled may be useful to ensure you did everything right.
Also consider how much memory your system might have in doing such a
calculation, or writing such a matrix. Also consider read/write permissions on
the working directory.
-Justin
On 11/20/08, *vivek sharma* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi All,
I am analyzing the h-bond information for a mdrun using g_hbond. Can
I know the % of trajectory time for which a bond between particular
residue was existing?
If anybody have tried such option please suggest me a way to do so.
With thanks,
Vivek
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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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