Hi,
when I minimize a system for 100 steps with nstxout set to 1 I expect to
get a trajectory with 100 frames.
However, gmxcheck reports 85 frames only and prints several weird
messages that several timesteps don't match.
Why is that?
Tested with gromacs 4.6.5 and 5.0, serial run as well as a
There are a few review article where the strategy and guidelines are described.
You can find this material on the cgmartini.nl website.
On Aug 29, 2014, at 2:03, Sridhar Kumar Kannam srisri...@gmail.com wrote:
Dear Gromacs users,
I have very recently started working with Gromacs and
On Fri, Aug 29, 2014 at 10:05 AM, Oliver Schillinger
o.schillin...@fz-juelich.de wrote:
Hi,
when I minimize a system for 100 steps with nstxout set to 1 I expect to
get a trajectory with 100 frames.
nsteps is the maximum number of steps. If mdrun decides it can't make
further progress, it
On Thu, Aug 28, 2014 at 11:59 PM, Siva Dasetty sdas...@g.clemson.edu
wrote:
Dear all,
Can we use periodic boundary conditions in case of implicit solvent
simulations?
Yes (but I only recommend doing so in GROMACS 4.5.x)
If so, why?
In general, why not? It's a boundary condition. What's
Ok yes, I got that.
I should have made it clearer.
The minimization actually run for 100 steps and did not converge.
But that is a different issue.
My probelm is that it run for 100 steps according to the log file, but
there are only 85 frames in the trajectory file even though nstxout was
set
Hi everyone. Does anyone know of any function in GROMACS or other MD program
for generating X-ray diffraction patterns?
/ Cyrus
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Dear users,
I recently try to run Gromacs on two nodes, each of them has 12 cores and 2
GPUs. The nodes are connected with infiniband and scaling is pretty good
when no GPU is evolved.
My command is like this:
mpiexec -npernode 2 -np 4 mdrun_mpi -ntomp 6
However, it looks like Gromacs only
Hi Dawei,
the mapping of GPUs to PP ranks is printed for the Master node only,
but if this node reports two GPUs, then all other PP ranks will also
use two GPUs (or an error is reported).
The scaling will depend also on your system size, if this is too small,
then you might be better off by
Hello,I want to calculate PMF of DNA and lipid bilayer. DNA is 4.5 nm from the center of bilayer at t=0. I use the pull-code to bring closer DNA to the bilayer .This is my mdp.file: pull = umbrellapull_geometry = cylinderpull_dim = N N Ypull-r1
Hi Dawei,
On 29 Aug 2014, at 16:52, Da-Wei Li lida...@gmail.com wrote:
Dear Carsten
Thanks for the clarification. Here it is my benchmark for a small protein
system (18k atoms).
(1) 1 node (12 cores/node, no GPU): 50 ns/day
(2) 2 nodes (12 cores/node, no GPU): 80 ns/day
(3) 1 node
Hi GROMACS users,
GROMACS 4.6.7 is officially released. It contains a few bug fixes,
particularly with regard to correctness of hybrid MPI/OpenMP PME
simulations at moderate-to-high parallelism. We encourage all users to
upgrade their installations from earlier 4.6.x releases, particularly from
Dear Users,
I am doing an umbrella sampling for a protein-ligand complex, wherein I
first did an SMD run for 500 ps and generated 500 configurations, the COM
distances for these configurations start at 1.25nm for conf0 and so on till
6.4nm for conf500. Hence I used a 0.05nm spacing to select
On 8/29/14, 2:08 PM, Mana Ib wrote:
Dear Users,
I am doing an umbrella sampling for a protein-ligand complex, wherein I
first did an SMD run for 500 ps and generated 500 configurations, the COM
distances for these configurations start at 1.25nm for conf0 and so on till
6.4nm for conf500.
Hi,
On Fri, Aug 29, 2014 at 4:19 AM, Bin Liu fdusuperstr...@gmail.com wrote:
I am recently puzzled by the syntax and behaviour of g_select. I want to
obtain the residue index list of LIPID whose center of mass is within 1.0
nm of the surface of protein. In my case, each LIPID molecule
14 matches
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