On 5/11/2010 10:48 PM, bharat gupta wrote:
I followed the same instructions given in the gromacs manual , step by
step ... I first tried installing gromacs with the first command given
in the manual and then again I installed with the options for FLAGS
but finally ended up with the following er
On 6/11/2010 4:02 PM, bharat gupta wrote:
Hi all ,
Whenever i am running the genbox command I am getting the following
error :-
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
:-) G R O M A C S (-:
Segmentation fault (core dumped)
yes the first two commands namely - pdb2gmx and editconf are working ...
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-368
On 4/11/2010 11:04 PM, Justin A. Lemkul wrote:
Carla Jamous wrote:
Hi everyone,
I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg
What I don't understand is why there are 3 columns in the file
resarea.xvg although this is what's written in my file:
# g_sas is part of G R
Hello,
Hopefully someone can help me understand how to use the mdrun -rerun
functionality, because currently I am confused. I would like to be able to
look up potential energy values for a number of conformations by calling
mdrun -rerun once.
The idea to use mdrun -rerun is from advice given to m
Hi,
You need to use md integrator for -rerun to work.
Good luck,
Chris
2010/11/6 Martin Kamp Jensen
> Hello,
>
> Hopefully someone can help me understand how to use the mdrun -rerun
> functionality, because currently I am confused. I would like to be able to
> look up potential energy values f
Hi Chris,
On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk
wrote:
> Hi,
>
> You need to use md integrator for -rerun to work.
>
Aha, now it seems to work. Thanks!
I am just sad that I did not find that information. According to
http://manual.gromacs.org/current/online/mdrun.html "With -reru
You can try the systems we provided on the GROMACS-GPU page:
http://www.gromacs.org/gpu#GPU_Benchmarks
--
Szilárd
On Sat, Nov 6, 2010 at 12:59 AM, lin hen wrote:
> Yeah, I think my problem is the input, but I don't have the .mpd file, I am
> using the existing input which has no problem with
Hello,
No, the hole don't correspond to parts of the protein sticking out on the
other side. The protein is in the center of the box and the holes are not
due to pbc issues.
Diana
On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar wrote:
> Hey,
>
> Do the holes match the parts of the protein s
Hi Martin,
Well, I was browsing the source code just yesterday cause I also noticed
that with steep integrator mdrun does not notice -rerun presence. And it
turned out that in do_steep() no one cares if -rerun is on. And if you think
for a moment what it does, it makes sense. However, it would be
Hi Diana,
Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
reading, sorry. But are these holes created by genbox, or are they already
present in the acn solven box? Have you already checked all intermediate
structures?
Cheers,
Tsjerk
On Nov 6, 2010 7:25 PM, "Diana Lousa" w
Hi,
It seems to me that the holes are created by genbox because I don't have
them in the original solvent box. The intermediate box (outputed by trjconv)
with the protein solvated but not converted is difficult to analyze, because
the box doesn't have the right shape and of pbc issues, but it seem
Hi Diana,
Does it also happen if you solvate the box without the protein? And are the
holes close to the protein or just anywhere? And what makes it difficult to
analyze the structure output by genbox directly, perhaps specifying that the
output be .pdb? It's what I usually do.
Cheers,
Tsjerk
O
Holes... Holes... What is the size of these holes? Use g_density,
g_rdf, make plots, observe peaks...
> Hi Diana,
>
> Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
> reading, sorry. But are these holes created by genbox, or are they already
> present in the acn solven box
Hi,
I have scaled the non-bonded parameters(charges and epsilon) of tip3p atoms
in ffnonbonded.itp file(charmm forcefield). They are scaled by a ratio of
3/5. The simulation is then run at 500K for the protein water system. The
temperature exploded after first 20 steps. This does not happen if I r
I suspect that you need to re-equilibrate your box volume to the new
solute parameters -- the volume probably needs to increase. Run a
simulation with a much smaller timestep and the Berendsen barostat and
the SD integrator. If this is stable, then use the output coordinates
of that to star
On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:
Hi Chris,
On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk
mailto:mitomas...@gmail.com>> wrote:
Hi,
You need to use md integrator for -rerun to work.
Aha, now it seems to work. Thanks!
I am just sad that I did not find that infor
> Hi,
>
> I have scaled the non-bonded parameters(charges and epsilon) of tip3p atoms
> in ffnonbonded.itp file(charmm forcefield). They are scaled by a ratio of
> 3/5.
What's the idea behind this scaling please?
>The simulation is then run at 500K for the protein water system. The
> temperature
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