Michael,
thanks for suggestions.
the main reason of ussage N-H with chains is the assumption that simple N-H
does not provide ergodicity of the system assuming that I'd like to sample
all temperature acceptable conformations on the 100 ns trajectory.
But as I understood the chain regime does
Dear GMX users,
I' d like to put the position restraints on water oxygen atoms.
To do so, I made a water_posre.itp file. Then I modified the top file, as this,
but didn't work:
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx
On 2013-06-02 06:40, Marcelo Vanean wrote:
*On 2013-06-01 17:11, Marcelo Vanean wrote:
*
*On 2013-06-01 02:24, Marcelo Vanean wrote:
*
*Hello to everyone. In version 4.5.5, calculating the viscosity with the
command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
visco.xvg)
Hello everyone.
During the calculation of the rms with g_rmsdist command , the reference
and the current structure are aligned before calculating??
Regards,
--
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
--
gmx-users mailing list
What's in that .itp? You can only restrain all the waters that have that
moleculetype. See
http://www.gromacs.org/Documentation/How-tos/Position_Restraints
On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Dear GMX users,
I' d like to put the position restraints
-append is the default behaviour. You can turn it off. But you can't turn
it off and have behaviour like it is on. You will need to deal with your
file size problem yourself by concatenating files later on, if you need to.
Mark
On Sun, Jun 2, 2013 at 6:14 AM, vidhya sankar
See g_rmsdist -h
Mark
On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele nawel.m...@gmail.com wrote:
Hello everyone.
During the calculation of the rms with g_rmsdist command , the reference
and the current structure are aligned before calculating??
Regards,
--
*Mlle* Mele Nawel
Master 2 In
Hi,
THanks for your answers. I already seen the help for this command but when
its write
g_rmsdist computes the root mean square deviation of atom distances, which
has the advantage that* no fit is needed* like in standard RMS deviation as
computed by g_rms what mean excatly no fit is needed??
I just applied genrestr command:
#genrestr -f minim.gro -o water_posre.itp -fc 10 10 10
And then I just chose the water to create the water_posre.itp.
Would not that work?
Sincerely,
Shima
From: Mark Abraham mark.j.abra...@gmail.com
To: Shima
Dear Gromacs user Thank you for your previous reply
When i Compile gromacs 4.5.6 I have Gor following error
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving
And I my point was I didn't think that there was going to be a
measurable ergodicity difference between NH chains and NH. Given the
size of the system, the chaoticness of atomic motions will likely give
you configurational sampling indistinguishable from full ergodicity.
Most of the errors that
On 6/2/13 9:03 AM, vidhya sankar wrote:
Dear Gromacs user Thank you for your previous reply
When i Compile gromacs 4.5.6 I have Gor following error
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/root/gromacs-4.5.6/src/kernel'
make[2]:
On 6/2/13 7:57 AM, Shima Arasteh wrote:
I just applied genrestr command:
#genrestr -f minim.gro -o water_posre.itp -fc 10 10 10
And then I just chose the water to create the water_posre.itp.
Would not that work?
No, it won't. You can't run genrestr on a configuration with
Mark,
could you also provide me with some examples when usage of VS could give
artifacts in simulations ?
In particular I'm interesting in usage of VS on hydrogens with membrane
proteins.
James
2013/6/1 James Starlight jmsstarli...@gmail.com
Thanks for so detailed explanation!
I've also
Hi
I am tyring to compute total virial, i.e. sum_i sum_j (rij*Fij). To achieve
this, I am making modifications in the gmx_nb_generic_kernel() function in
nb_generic.c. In it, I see that atoms I and j are accessed from neighbor
lists to determine forces on atom I . My question is that in this loop
Hi Nawel,
g_rmsdist calculates the RMSD of distances, and distances are invariant to
translation and rotation.
Cheers,
Tsjerk
On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele nawel.m...@gmail.com wrote:
Hi,
THanks for your answers. I already seen the help for this command but when
its write
I've always wondered why people do this. There are no pi electrons in your
force field so it seems to me that if you find a stable cation-pi interaction
in your simulations then that just implies that a real cation-pi interaction is
not necessary to stabilize this particular conformation. That
On Sun, Jun 2, 2013 at 4:56 PM, James Starlight jmsstarli...@gmail.comwrote:
Mark,
could you also provide me with some examples when usage of VS could give
artifacts in simulations ?
I don't know of any particular examples. This kind of thing tends to be
tested ad hoc - how far can the time
Chapter 8 of the manual names a tool that sounds like what the OP wants ;-)
Mark
On Sat, Jun 1, 2013 at 10:25 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
Can g_angle not handle this?
Dr. Vitaly Chaban
On Sat, Jun 1, 2013 at 10:15 AM, larif sofiene larifsofi...@gmail.com
wrote:
Hello everyone. I want to know if can be applied pressure coupling only in
the z direction, allowing the edges x and y simulation box with fixed size.
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
Hi all
I want to simulate protein-fatty acid-AU complexs by OPLSAA force field. But
OPLSAA force field, hasn't any parameter for fatty acid. Can I use CHARMM fatty
acid parameters in OPLSAA force field? Anyone has better suggestion?
Fatemeh Ramezani
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gmx-users mailing list
Off subject, I thought a good pop up for the end of file processing etc...would be
___
Government spies are everywhere, theyre in your home, theyre in your hair
theyre down the street and hiding in walls
Theyre waiting to take you away Fabulous flying
Hi GROMACS Users,
These days, I am testing restarting simulaitions with .cpt files. I already set
nlist=1 in the .mdp file. I can restart my simulations (which are stopped
manually) with the following commands (version 4.0.7):
mpiexec mdrun_s_mpi -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md
Hi GMX users!
I just completed my first 30 ns simulation and would to remove all water
molecules from the resulting .gro and trajectory files for the sake of my
HDD.
Does anyone know how to do this?
Cheers,
Parker
--
gmx-users mailing listgmx-users@gromacs.org
trjconv for trajectories
editconf for coordinate files
Along with an appropriately generated index file (using make_ndx) which
contains the molecules you want in the output within a single group.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences,
Thanks Warren for your help, those were exactly the functions I was looking
for!
However I'm still experiencing a bit of trouble because my simulated
protein contained a heme cofactor and it seems to only let me extract one
object.
Have you had any experience with this?
Parker
On Sun, Jun 2,
What group did you select from the list offered when you ran the script? Did
it include all of your molecules, minus water? Or did you just select
something like Protein?
You need to run make_ndx and general a group that contains all of the molecules
you want. So you will want to do
FYI you can also take the complement of an existing group with make_ndx
using the ! symbol.
e.g. if water is group 0, you could make a group of everything but water
using:
!0
This might be easier/more foolproof than concatenating all other groups
when generating the appropriate index file as
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