Dear Raman,
1. For using GPU enabled gromacs, the gromacs must be installed using
-DGMX_GPU=ON
flag.
2. The commands are all same as with the non gpu enabled ones. For running
the mdrun program, you need to incorporate
cutff-scheme = verlet in the mdp file (Details can be viewed at
Dear gromacs users,
I posted a similar question the other day, but it was probably too long, so
here it is more concisely:
I've taken the ascii output of g_covar and built the 3N x 3N covariance matrix
in MATLAB from the 3N^2 x 3 matrix, which I've then normalized to get a 3N x 3N
cross
Hi everybody,
I wrote last week, but nobody answered. So I write again, still having the same
problem:
I want do an analysis of my simulation with the tool g_chi.
The problem is, that the optional output options don't work.
I use the following command:
g_chi -s config.gro -f traj.xtc -oh
Thanks Amin and Chandan for these helpful tips. I have now successfully
installed GPU enabled Gromacs. Hope to have some fun in running faster
simulations.
Regards,
Raman
On 9 July 2014 15:07, Chandan Choudhury iitd...@gmail.com wrote:
Dear Raman,
1. For using GPU enabled gromacs, the
On 7/9/14, 3:56 AM, Yana Tsoneva wrote:
Dear colleagues,
I am running simulations using Gromacs - 4.6.5 and my systems consist of
water/different oils. Until now I have used TIP4P water model and amber99
for the alkanes.
I need to run the same simulations, but with a polarizable water model.
On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
hello every one
I am working on complex with popc membrane i did
perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
after this step minimization
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
i got error
Fatal
Hello again,
This what I have been trying to do so far. This is the command to run the
script:
./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff
and this is the error I have been getting along with 2 Notes:
NOTE2: Please be sure to use the same version of CGenFF in your
BSD
Dear Szilárd,
Thanks very much for your reply.
This compiler is very outdated, you should use at least gcc 4.7 or 4.8
for best performance - especially the CPU-only runs should get quite a
bit faster.
Thanks, point taken. The person who compiled this on the test machine just
used what
Dear gromacs users,
i am using gromacs 4.6.2. i tried the secondary structure analysis, using
do_dssp. but i got the following error.
Fatal error:
Failed to execute command: /usr/local/bin/dssp.exe -na ddFyZGQ1 ddTj0ABl
/dev/null 2 /dev/null.
i am using amd, with cemtos. i downloaded dssp
Hello people,
is there any way of pass what group of solvent I want to use in *genion*?
I'm creating a non-interactive script that calls genion, any thoughts about
how I would solve it?
Thanks!
Marco.
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Dear Teemu,
I have been following one of your presentations on Improved Gromacs
analysis using dynamic selections and also referring your publication on
LDL modeling and dynamics. My simulation system is quite similar to your
LDL model. In your presentation I came across the following dynamic
On 7/9/14, 5:51 AM, Anna Stopka wrote:
Hi everybody,
I wrote last week, but nobody answered. So I write again, still having the same
problem:
I want do an analysis of my simulation with the tool g_chi.
The problem is, that the optional output options don't work.
I use the following command:
On 7/9/14, 8:37 AM, Uma Devi wrote:
Dear gromacs users,
i am using gromacs 4.6.2. i tried the secondary structure analysis, using
do_dssp. but i got the following error.
Fatal error:
Failed to execute command: /usr/local/bin/dssp.exe -na ddFyZGQ1 ddTj0ABl
/dev/null 2 /dev/null.
i am using
On 7/9/14, 8:46 AM, Marco Rougeth wrote:
Hello people,
is there any way of pass what group of solvent I want to use in *genion*?
I'm creating a non-interactive script that calls genion, any thoughts about
how I would solve it?
genion works like any other command in that regard.
On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote:
Thanks for the reply Justin. I just checked my box size again and found it to
be smaller than the required. Hence I changed the size and ran the simulation
again. This time energy minimization happened correctly without any change in
the graphene
That's the answer! Thank you Justin.
Marco.
2014-07-09 14:25 GMT-03:00 Justin Lemkul jalem...@vt.edu:
On 7/9/14, 8:46 AM, Marco Rougeth wrote:
Hello people,
is there any way of pass what group of solvent I want to use in *genion*?
I'm creating a non-interactive script that calls
Hi gromacs users and developers,
I have troubles with simulations of the system with surface (slab geometry)
using GPU and Verlet cut-off scheme.
When I run this simulation on CPU everything goes right and ions dissolved
in the water above the surface seems to behave normally. But when I switch
to
Hi Justin,
Do you plan to keep the Gromacs 4.x versions of your tutorials (which by
the way are excellent) around for a little longer as well?
From my experience It will still take quite some time until Gromacs 5 is
available on most Clusters and Linux-package repositories, whereas the
Gromacs 4
On Jul 9, 2014 7:39 PM, Ondrej Kroutil okrou...@gmail.com wrote:
Hi gromacs users and developers,
I have troubles with simulations of the system with surface (slab
geometry)
using GPU and Verlet cut-off scheme.
When I run this simulation on CPU everything goes right and ions dissolved
in the
Hello Gromacs Users,
Can the atom field (e.g., H) of a .top / .itp file differ from the atom
field of the .gro file and, for instance, the ffnonbonded.itp file? What
are the restrictions here?
My guess is that the .top /.itp will reference with the ffnonbonded.itp
with the type field only
On 7/9/14, 2:40 PM, Oliver Stueker wrote:
Hi Justin,
Do you plan to keep the Gromacs 4.x versions of your tutorials (which by
the way are excellent) around for a little longer as well?
From my experience It will still take quite some time until Gromacs 5 is
available on most Clusters and
On 7/9/14, 5:08 PM, Eric Smoll wrote:
Hello Gromacs Users,
Can the atom field (e.g., H) of a .top / .itp file differ from the atom
field of the .gro file and, for instance, the ffnonbonded.itp file? What
are the restrictions here?
My guess is that the .top /.itp will reference with the
Hi Justin,
I did simulation 2 times, once with PBC in xy with walls and other time with
pbc in xyz.
For pbc in xy with walls with following wall parameters:
nwall = 2
wall_type = 12-6
wall_density = 5 5
wall_atomtype = opls_995 opls_996
wall_r_linpot = 1
wall_ewald_zfac = 3
Energy
Dear all,
I want to carry out umbrella sampling on a protein-ligand complex, that was
already subjected to regular MD simulation for a few nanoseconds.
How should I calculate the optimum pull distance and box size to be used?
Is there a default value that can be applied?
Also how to calculate
Thank you Sir. gmx help explains it. I tried to compile the tools on
gromacs-4.5 but somehow the installation was terminating with errors. Then
I thought, you might have the modified gromacs copy. Anyway, I will try to
install the tools on gromacs-4.5 template. Thank you sir for your time and
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