Hi,
> On 25. Feb 2019, at 21:15, Schulz, Roland wrote:
>
> That's not my experience. In my experience , for single node runs, it is
> usually faster to use 72 OPENMP threads rather than using 72 (t)MPI threads.
wouldn’t a combination of OpenMP threads * (t)MPI threads be faster, e.g. 8x9?
Cars
Dear Kevin,
Thank you for your reply.
I did 2 tests:
1- I wanted to see in details when the system crashes and which atoms are
involved so I restarted the simulation from the checkpoint but using a new mdp
file. The only parameter that I changed was nstxout-compressed = 1. In this
case, the s
Dear gmx comunity,
I have tried to get the last structure from a trajectory using:
gmx_d trjconv -pbc mol -ur compact -s topol.tpr -f traj_comp.part0001.xtc
-o out.gro -n index.ndx -dump -1
But I get the first structure. Maybe the -1 syntax that is used in python
for example does not work her
You have to dump the last frame: for example* -1 *for a 1ps/10ns
trajectory
On Tue, Feb 26, 2019 at 4:31 PM Sergio Perez wrote:
> Dear gmx comunity,
>
> I have tried to get the last structure from a trajectory using:
>
> gmx_d trjconv -pbc mol -ur compact -s topol.tpr -f traj_comp.part
For continuing a normal MD simulation (with -deffnm test) crashed by wall
time I use "...-deffnm test... -cpi test.cpt -append" and everything is
fine.
Now I will do the same for a pulling simulation where the -deffnm is pull
where the coordinate and force are named pull_pullx.xvg and pull_pullf.xv
Hi all,
I am simulating my protein with Alpha-Ketoglutarate and I have been searching
literature on ways to parameterise the molecule for the AMBER FF. I'm not
having any luck and was wondering if anyone has or knows how to parameterise
Alpha-Ketoglutarate? The chemical formula is C5H4O5-2.
An
usually, I use acpype to generate parameters for AKG and using Gaussian to
calculate partial charges
On Tue, Feb 26, 2019 at 2:33 PM Pandya, Akash
wrote:
> Hi all,
>
> I am simulating my protein with Alpha-Ketoglutarate and I have been
> searching literature on ways to parameterise the molecule
On Mon, Feb 25, 2019 at 9:15 PM Schulz, Roland
wrote:
> That's not my experience. In my experience , for single node runs, it is
> usually faster to use 72 OPENMP threads rather than using 72 (t)MPI threads.
>
I believe that will depend on system size, compiler (with gcc/gomp wide
ranks are slow
Yes, I understand that, in that case you know how long the simulation is.
But what if I don't know how many frames the simulation has can I access
it directly? Or do I need to do a gmx check to see how long the trajectory
is?
On Tue, Feb 26, 2019 at 12:11 PM aditi singh wrote:
> You have to dum
Dear all,
I have done the MD simulation of protein-water-osmolyte. Now I want to
calculate the number of hydrogen bond formed between water and osmolyte in
the first hydration shell of the protein. Can anyone tell me how to
calculate this?
Do I have to make the index of water and osmolytes molecule
My protein Fab has VH, VL, CL, CH domains. Usually in the RMSD calculation, I
align the whole Fab first, then use a index file to calculate the domain's RMSD:
$ echo 1 19 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n
index.ndx
(Group 1 is the whole protein, Group 19 is one of
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html
http://manual.gromacs.org/documentation/2019.1/onlinehelp/selections.html
http://manual.gromacs.org/documentation/2019.1/onlinehelp/selections.html#selection-examples
Select water and osmolyte within the specified distance
Hi,
Unfortunately there is no simple way to get the last frame. Even gmx
trjconv -dump doesn't help unless you know quite well what time you seek.
So gmx check is your friend.
Mark
On Tue, 26 Feb 2019 at 08:08 Sergio Perez wrote:
> Yes, I understand that, in that case you know how long the sim
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