On 9/1/19 7:02 AM, m g wrote:
Dear Justin,
There are many other people on this list, and I don't always have answers :)
I'm simulating a system with "wall" for z direction, but I gave this error in
minimization step "software inconsistency error: lost particles while sorting",.Would you
On 9/1/19 5:44 AM, Avijeet Kulshrestha wrote:
Hi all,
I am running martini coarse-grained simulation with 15 fs of time step in
gromacs 2018.6. I have 25859 number of atoms and my box size is:
12.0 14.0 18.0
Where I have Protein, membrane (DPPC) and ions.
I have minimized energy
On 9/1/19 5:35 AM, Negar Parvizi wrote:
Dear all,
I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my
file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is
Thanks Justin. The problem has been fixed.
On Fri, Aug 30, 2019 at 7:31 AM Justin Lemkul wrote:
>
>
> On 8/29/19 12:31 PM, Prabir Khatua wrote:
> > Hello Gromacs users,
> >
> > I am trying to simulate a system of atom size 3,58,973 in gromacs 5.1.5.
> > However, my simulation is being
Dear all,
I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for
my file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is in z direction.what should I do now
for wham
Dear Justin, I'm simulating a system with "wall" for z direction, but I gave
this error in minimization step "software inconsistency error: lost particles
while sorting",.Would you please help me? I used the following parameter:
integrator =steep
emtol = 100.0emstep
Dear all,
I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my
file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is in z direction.what should I do now
for wham
Hi all,
I am running martini coarse-grained simulation with 15 fs of time step in
gromacs 2018.6. I have 25859 number of atoms and my box size is:
12.0 14.0 18.0
Where I have Protein, membrane (DPPC) and ions.
I have minimized energy with 16 processor and -rdd option as 2.5. It
