Dear gxm users,
Now I am doing solvation free energy of a protein, I follow Sander Pronk's
tutorial downloaded from Gromacs page.
1. How do I check system is equilibrated?
2. I run following command
sh mklambdas.sh run.mdp topol.top equil.gro
I got following error:
mklambdas.sh: 12:
Hi Justin and all,
Meanwhile, is it possible to implement a self-consistent FF from scratch? One
example I came across is from the work by Ho and Striolo
titled: Polarizability effects in molecular dynamics simulations of the
On 10/13/14 10:42 PM, Nilesh Dhumal wrote:
hello,
I running grompp for simulation. I get Segmentation fault error.
grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr
checking input for internal consistency...
processing topology...
Segmentation fault
Could any one tell what is the
On 10/14/14 12:31 AM, RINU KHATTRI wrote:
hello gromacs user i am working on protein ligand complex with popc membrane
i am running production md in extended time (40 ns) i got some file i
am using -noappend option i got confout.gro file in each extended time
what is the use of this file if i
On 10/14/14 7:40 AM, Kester Wong wrote:
Hi Justin and all,
Meanwhile, is it possible to implement a self-consistent FF
from scratch? One
example I came across is from the work by Ho and Striolo
titled: Polarizability effects
Dear Mark and ALL,
I am trying to calculate the conserved energy (H-tilde) in Bussi's
stochastic velocity rescale algorithm (jcp,2007).
In previous maillist, Mark had mentioned that the conserved En. in ener file
is the H in bussi's paper
Thank you Mark for the reply,
We use pbs for submitting jobs on our cluster and this is how I request the
nodes and processors
#PBS -l
select=2:ncpus=8:mem=8gb:mpiprocs=8:ngpus=2:gpu_model=k20:interconnect=fdr
Do you think the problem could be with the way I installed mdrun using Open
MPI?
Dear gmx-users,
Hello, I am working on free energy calculation of a protein. How long run
should be enough for Free Energy Calculation of a protein?
Batsaikhan
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Hi users,
I am trying to simulate 2-d liquids interacting with simple potential like
Lennard-Jones potential.
Can it be done by specifying pcoupletype = semiisotropic in the .mdp
file? I mean enforcing a normal pressure in x-y direction while very high
pressure in z direction to constrain the
Hello,
I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded
in POPC lipid membrane. After energy minimizing of complex, I am facing
problem with NVT equilibration step. mdrun crashed with following error:
12 particles communicated to PME node 4 are more than 2/3 times the
Try: mpirun -npernode 2
-Trayder
On Wed, Oct 15, 2014 at 8:42 AM, Siva Dasetty sdas...@g.clemson.edu wrote:
Thank you Mark for the reply,
We use pbs for submitting jobs on our cluster and this is how I request the
nodes and processors
#PBS -l
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