Hi,
may I ask how do you get the potential energies from a simulation? Is it
possible to get continuous energy-time graph for a system?
thanks in advance
Jan Neumann
David Mobley schrieb:
> Maybe this is what someone is getting at in their answers, but you
> COULD sort of "invert" the problem: U
Dear all,
I try to get an MD simulation running of a serin protease where the
active site serin is inhibited by Diisopropylfluorophosphate (DFP). I
know there is a topology for phosphoserin but how do I get a topology
for the additional isopropyl groups and how do I treat this "special"
amino
Dear All,
While analysing one of the trr files using g_order I
am getting two NANs (not a number) in the deuter.xvg
and order.xvg between an interval of 1ns. (specified
by using -b and -e command).
what does this signify and why is this happening? Does
this show that there is some problem with th
Dear sirs: How to calculate the probability of conformational distributions in gromacs by PCA method? I often meet it, but I do not know how to define it! The free energy = -KBTln(probability of conformational distribution). Thank you for your reply!
Mp3疯狂搜-新歌热歌高速下
xi zhao wrote:
Dear sirs:
How to calculate the probability of conformational distributions in
gromacs by PCA method? I often meet it, but I do not know how to define
it! The free energy = -KBTln(probability of conformational distribution).
g_sham
Thank you for your reply!
--
I'm still having problems with g_hbond. I've submitted a bugzilla report.
- The hbond existence matrix in the -hbm output does not match the list of
hbonds in the ndx file from -hbn.
- Also, it outputs "No option -g" when no -g command line option has been
tried
- Also, sometimes the number of
> may I ask how do you get the potential energies from a
> simulation? Is it possible to get continuous energy-time
> graph for a system?
Use the script g_energy on the .edr file from the simulation.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Vic
With Giovanna's help I was able to complete a grompp
run on my system. I did, however get a warning:
WARNING 1 [file "topol.top", line 12]:
Bad box in file Complex.GRO
Generated a cubic box 20.000 x1.445 x1.830
What does this mean? Line 12 refers to one of my
complex molecules under t
Here's what I've been able to do so far . . .
1. Generated a two molecule complex and saved as .pdb
2. Parsed the file out to retain relative coordinates
of each molecule in separate .pdb files
3. Run both resulting molecules through PRODRG server
to generate .gro files for GMX processing.
4.
Hi Marc,
The .gro format should contain:
1 line with title/comment
1 line specifying the number of atoms (n)
n lines with atom coordinates
1 line with the box specification
For a rectangular box, the box specification is just three free
format floating-point numbers (x,y,z axes).
Gromacs ca
Dear all,
My question is on the theory of MD. I actually could not find any material
which describes in detail about the time integration algorithm.
1) I wanted to know why the time integration algorithm has to be used,
I mean the practical benefits of it. I want the reading reference for the
s
Hi,Two reading suggestions:1. Allen & Tildesley, Computer Simulation of Liquids, ISBN 01985564542. Frenkel & Smit, Understanding Molecular Simulations, ISBN 0122673514Cheers,ErikOn Aug 23, 2006, at 1:54 PM, [EMAIL PROTECTED] wrote:Dear all,My question is on the theory of MD. I actually could not fi
Hi!
On 8/23/06, Marc Charendoff <[EMAIL PROTECTED]> wrote:
With Giovanna's help I was able to complete a grompprun on my system. I did, however get a warning:
WARNING 1 [file "topol.top", line 12]:Bad box in file Complex.GROGenerated a cubic box 20.000 x1.445 x1.830
are you sure this me
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