I would like to run one simulation in parallel so that it utilises all the
available nodes and cores. For that,
I have compiled gromacs with mpi enabled and also installed openmpi on my
machine.
I am using the following command:
mpirun -np 4 mdrun_mpi -v -s *.tpr
When i use top command, I get:
PI
All,
Below is some code I wrote a few years ago during my PhD. I started with a list
of bonds in a file called 'bonds' and t he used this list to automatically
create the lists of angled and proper dihedrals. I went on to edit this code to
create a topology for entire polymers based on a single
Hi,
Is it a local work station or cluster with multiple CPUs? Which gromacs
version did you install?
On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor
wrote:
> I would like to run one simulation in parallel so that it utilises all the
> available nodes and cores. For that,
> I have compiled gromac
Hi,
I have used Grid-Mat program for calculating bilayer thickness and area per
lipid for POPC bilayer.
For bilayer thickness, without peptide, it provides the lateral area of
system in angstrom sq. and also APL. (keeping APL as no)
I separately calculated the APL with peptide, It also provides
On 10/7/13 8:00 AM, Archana Sonawani-Jagtap wrote:
Hi,
I have used Grid-Mat program for calculating bilayer thickness and area per
lipid for POPC bilayer.
For bilayer thickness, without peptide, it provides the lateral area of
system in angstrom sq. and also APL. (keeping APL as no)
I separa
Dear Chris,
Thank you for your message. I uploaded everything to the redmine. I will
let you know how the simulation with generated velocities went.
I asked the authors about any exemplary input that worked with tip5p and
oplsaa, but I did not get anything...
Best,
Grzegorz
On 2013-10-04 17:2
To add : I am running simulations on institute cluster with 8 nodes (2
cores each).
Please suggest me the way so that I can run one simulation on all available
nodes, cores and threads.
Thanks in advance.
On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor
wrote:
> I would like to run one simulatio
Hello All,
I have calculated the distance between the binding pocket of protein and
the ligand molecule but due to ligand diffusion out of box, I am getting
wrong distance as first it increases till 5nm and then decrease again to
around 1nm during the simulation (which is not possible).
I have fi
On 10/7/13 10:46 AM, bipin singh wrote:
Hello All,
I have calculated the distance between the binding pocket of protein and
the ligand molecule but due to ligand diffusion out of box, I am getting
wrong distance as first it increases till 5nm and then decrease again to
around 1nm during the si
You need to contact your cluster administrator for instructions of how to
submit jobs to the cluster. Usually you have to create some kind of
shell-script that specifies various parameters of your job and then submit it
to a queue system.
Below you submitted the job most likely to the 'head-nod
Thanks for the reply Dr. Justin.
I have also thinking of the same possibility but to further confirm, I am
sending the link for the plot of the distance between the COM of ligand
binding pocket and COM of ligand molecule, please find some time to have a
look at the plot and let me know if it seems
On 10/7/13 1:39 PM, bipin singh wrote:
Thanks for the reply Dr. Justin.
I have also thinking of the same possibility but to further confirm, I am
sending the link for the plot of the distance between the COM of ligand
binding pocket and COM of ligand molecule, please find some time to have a
lo
Hello Gromacs users,
I want to obtain the topology file (topol.top) for this peptide
Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2.
I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb
-o pep5-dpp-cap-linear-phospho_newbox_up_rotate.gro -ignh -ter -wa
On 10/7/13 4:40 PM, Villarealed wrote:
Hello Gromacs users,
I want to obtain the topology file (topol.top) for this peptide
Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2.
I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb
-o pep5-dpp-cap-linear-ph
Dear Justin,
Your are right, as usual.
Thank you so much.
-
Eduardo Villarreal RamÃrez
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/pdb2gmx-takes-ph
With a ligand diffusing as freely as I'm assuming (you've omitted a lot of
info, box size etc.) you aren't going to get PBC to play nice, although
-nojump should have atleast given you a different wrong answer.
Centering the system on the same point you are using to define the binding
pocket (may
Dear gmx-users,
I have just finished umbrella MD but I missed to type pullf/pullx options
on mdrun.
So, can I get pullf/pullx .xvg files from mdrun results?
Best regards,
Yoochan
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please sea
Dear All,
I am trying to follow lipid bilayer simulation tutorial,I am
getting struck at energy minimization same step after generating
system_inflated.gro file. I get the same error,
Fatal error:
Invalid line in system_inflated.gro for atom 6439:
25.67360 25.77400 6.59650
I checke
Thanks for the reply Dr. Trayder and Dr. Justin.
I have performed unrestrained MD with a ligand bound protein having surface
exposed binding pocket (link of the image attached for clarification). I
have used a cubic box with vectors 6.432nm and the system size was 4.117
3.878 and 4.059 (in nm).
h
Both cases are 'real' ligand binding. If a drug binds, it binds. It doesn't
matter how far away it comes from.
Each periodic image is identical, it's the same ligand capable of making
the same interactions in the same protein but approaching from a different
angle.
-Trayder
On Tue, Oct 8, 2013 a
20 matches
Mail list logo
