Dear All,
I would like suggestions on the following questions in Essential Dynamics
analysis. I have been working on the essential dynamics analysis of a 450
aa protein and its mutant.
To exclude the existance of random diffusion effects, I calculated cosine
content and found it to be very high
Dear All,
...I think I should generate an .ndx file with all the atoms
I need as well as the solvent molecules, but I have some basic problem
in understanding the preparation of .ndx file, when I am executing the
commnad make_ndx and select system, index file is being prepared, but
Hi Jochen:
Did you receive any responce??? I font 2 different parameters for NO. one of
2 sites and other of three sites. I try to build the three sithe model but I
can get it to work because I have problems with the third site, a dummy atom.
Probably you have more experience with GROMACS than
Thanks a lot to Dr Sica and Dr. Warren.
regards
Sangeeta
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Dear all,
I am testing the INM analysis. I get the eigenvector
file eigenvector.trr; and then do the projection on
INM normal modes by the command:
g_anaeig -proj -v eigenvector.trr -f c.gro -proj
proj.xvg
But what I get from proj.xvg is pretty stange. Except
the first few values, all of
Hello,
I was wondering if I could run a simulation in parts. I would like to
run a simulation for 100ps say, analyze it, and then sometime later continue
on for another 100ps. It seems like all I would need to do is take the
*.gro, *.trr, and *.edr files output from the first md simulation,
Mike,
You should use the tpbconv script.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
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When the
Hi toma0052.
toma0052 wrote:
Hello,
I was wondering if I could run a simulation in parts. I would like to
run a simulation for 100ps say, analyze it, and then sometime later continue
on for another 100ps.
You can. When you restart you simulation make sure you use a grompp.mdp
file
Hello,
I was wondering if I could run a simulation in parts.
Absolutely... running calculations on large computing facilities requires
the ability to interact with a queueing system that will give you only
finite lengths of time, so cut and paste is a necessary attribute.
I would like
Thanks very much to the folk who did all the hard work on GROMACS.
Yesterday I did a simulation of the nuclear receptor VDR for 1 nanosecond,
and, using Vega-ZZ for analysis, was able to identify the entrance tunnel
for the ligand. This is something I have been trying to do for several
Trevor Marshall wrote:
...when I tried to
compile the FFTW and GROMACS sources (with gcc 4.1) the Configure script
complains that this compiler doesn't recognize the MPI commands.
Is it possible to compile using gcc 4.1 so that I get an SMP system
using both cores of my CPU? Do I need a
Mark,
Thanks for your response.
Do you know of a 3.x version which does compile GROMACS / FFTW OK for a
core-duo? Can you help me with a gcc switch configuration which worked on
one of those compilers?
Sincerely
Trevor
At 09:51 PM 2/21/2007, Mark Abraham wrote:
Trevor Marshall wrote:
Trevor Marshall wrote:
Mark,
Thanks for your response.
Do you know of a 3.x version which does compile GROMACS / FFTW OK for a
core-duo? Can you help me with a gcc switch configuration which worked
on one of those compilers?
Sorry, I have no expertise here.
Mark
Hi Trevor,
You should be fine with compilers from the 3.3 series or 3.4. You
shouldn't really need to set specific switches other than --enable-mpi
in the .configure script.
By the way, since you're in need of speed, I think I could cut your
simulation volume by 33-50%, scaling linearly in the
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