Hi,
I am wondering how to test the conserved quantity in an NPT simulation fron
the ener.edr file. As you well know for npt with a Nose-Hoover thermostat
and a Parrinello-Rahman barostat, the conserved quantity is not just K+P,
but contains additional terms function of the additional npt
hi.. i have problem in installing gromacs in my macbook pro ( personal pc)
.. can anyone help me with this??
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On 10/24/14 6:32 AM, Suraya Abdul Sani wrote:
hi.. i have problem in installing gromacs in my macbook pro ( personal pc)
.. can anyone help me with this??
Not unless you tell us exactly what you're doing - exact cmake command, exact
error messages, etc.
In general, follow
Those conserved quantities are indeed included in the reported
information. For thermostats/barostats where there is such a quantity,
it's included in the .edr file.
On Fri, Oct 24, 2014 at 4:23 AM, Paolo Franz paolo.fr...@gmail.com wrote:
Hi,
I am wondering how to test the conserved quantity
Hi Suraya. I have succesfully installed Gromacs 4.5, 4.6, and 5.0 on my
macbook pro running OS X Mavericks, even with CUDA support.
I am not using apple compiler because apple compiler in Mavericks (clang
3.4) doesn't support OpenMP, that will cause many errors when compiling
gromacs (my
Thanks for yor reply, Mark.
At first i was sure that the problem was table-exension because when I
enlarge table-extension value, warning message didn't appear anymore.
Besides, i have successfully minimized and equilibrated the system
(indicated by Fmax emtol reached; and no error messages
On 10/24/14 8:31 AM, Nizar Masbukhin wrote:
Thanks for yor reply, Mark.
At first i was sure that the problem was table-exension because when I
enlarge table-extension value, warning message didn't appear anymore.
Besides, i have successfully minimized and equilibrated the system
(indicated
Hi,
I would like to post a question about simulating with Walls in gromacs
and using the Martini force field.
The question is very simple. I am trying to simulate a simple box of water
molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen
T-coupling and no pressure bath.
I am
Hi Tsjerk,
This is a very useful script. Just found a small bug that is only
noticeable if one is using higher -nlevels for the .xpm construction (in
g_rms, for example)
z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
should be
z = [colors[j[k:k+nb]] for k in range(0,nx*nb,nb)]
instead. At least
What about electrostatics? Ewald summation is probably the culprit here.
On Oct 24, 2014 12:05 PM, Ramon Reigada reig...@ub.edu wrote:
Hi,
I would like to post a question about simulating with Walls in gromacs
and using the Martini force field.
The question is very simple. I am trying to
Just one more question on that topic:
according to the Hoempage
(http://www.gromacs.org/Documentation/How-tos/Doing_Restarts - After a
crash), it used to be possible to resume a crashed run by employing
tpbconv and supplying the trr file. As I did not save my cpt-files,
would that still be an
Hi,
I would like to post a question about simulating with Walls in gromacs.
The question is very simple. I am trying to simulate a simple box of water
molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling
and no pressure bath.
I am trying:
pbc=xy
nwall =2
Hi,
I have a system consists of a box of water and a monolayer of polymer in
the center. I am trying to extract solvent molecules that have z
coordinates greater than 5 nm using g_select and output an index file.
Basically I want to separate my system into two portions: a box of waters
above the
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