Hi Christopher & Mark,
My simulation worked well with the parameters given by Christopher. The sd
integrator & lincs-order was fit in this situation while md integrator
still had lincs warnings. I'll continue my runs with sd.
Thank you very much for your help!
Best wishes,
Sidong
Message: 4
>
Hi,
Please get a non-PLUMED version working first. When you report a command
line, please copy and paste it, rather than type it out and make typos.
Probably you are running a version of GROMACS that was compiled to run on a
different kind of node, but you need to find out what kinds of nodes your
Hi Francesca,
Please contact me directly.
Best,
João
On Fri, Aug 12, 2016 at 8:23 AM, Francesca Lønstad Bleken <
francescal.ble...@sintef.no> wrote:
> Hi,
>
> Thank you Joao, Justin and Marlon for your answers.
>
> Joao, I have been looking at your article the last days as it explains
> very we
hi users,
I am trying to run a simulation in a 16 core node having 2 GPUs build
inside and I am using the following command --
gmx_omp_mpi_gpu mdrun -ntmpi 2 -ntopm 8 -s *.tpr ...
and I am getting the following error-
q/var/spool/sge/default/p01/job_scripts/5226: line 30: 25864 Illegal
inst
Dear Mark and Justin,
I've switched to function type 1 and the simulation runs. I thought the
function type would correspond to the type of the comb-rule and missed
the information given in the 5.8.1 section of the manual.
Thanks a lot!
Andreas
Am 12.08.2016 um 14:15 schrieb Justin Lemkul:
Hi GROMACS people!
You may be interested in some upcoming events related to GROMACS, both to
use and to develop code around. These come to you courtesy of the EU-funded
HPC Center of Excellence called BioExcel (http://bioexcel.eu/). We may also
have some other events next year, perhaps associated
there is no any errors messages if I run it from terminal for a specific
step Everything goes well
On 08/12/2016 03:46 PM, Mark Abraham wrote:
Hi,
Run job.whateveritis and see the error message.
Mark
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Hi,
Run job.whateveritis and see the error message.
Mark
On Fri, Aug 12, 2016 at 3:33 PM Albert wrote:
> Hello:
>
> I wrote all steps for Gromacs MD simulation in a .tcsh script. Then I
> submitted the job into the local GPU workstation by command line:
>
> nohup ./job.tcsh &
>
> However, I o
Hello:
I wrote all steps for Gromacs MD simulation in a .tcsh script. Then I
submitted the job into the local GPU workstation by command line:
nohup ./job.tcsh &
However, I obtained the following messages immediately:
nohup ./job.csh &
[1] 13433
No any steps is running after I submit the
Hi everyone
I am currently trying to perform a peptide-ligand (~4000 and 110 Da
respectively) simulated annealing study using gromacs (5.1.2) with Amber
force fields. Under the initial energy minimization step (minim.mdp and
nvt.mdp) I am finding that the step fails. It then kicks out pdb files,
Dear gromacs user,
In my normal MD simulation of adsorption of a short peptide into a solid
surface in water solution, my system is nicely equilibrating (after 1.5 ns
NPT using isotropic condition) to an average around 1 bar pressure which is
my desire.
However, in my PMF calculations in which I
On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote:
Hello Mark,
sorry for the confusion I've created. My system refers to a solute in water
(which has only LJ-parameters for the oxygen atom). Within the solute, there are
two approaches to deal with LJ-interactions:
1) intramolecular interactions (
Hello Mark,
sorry for the confusion I've created. My system refers to a solute in
water (which has only LJ-parameters for the oxygen atom). Within the
solute, there are two approaches to deal with LJ-interactions:
1) intramolecular interactions (including 1-4 and far-off interactions)
2) inte
dear All gromacs user,
i have finished all steps for preparing topology.
my doubt is, after simulation is any possible to show the error or
structural modification???
or warning error..
pls say suggestion...any one.
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Hi,
On Wed, Aug 10, 2016 at 9:27 PM Francesca Lønstad Bleken <
francescal.ble...@sintef.no> wrote:
> I am interested in a metalloenzyme with Cu and I have found several
> studies in the literature on systems similar to mine using GROMACS and the
> Gromos force field. I see that GROMOS contains pa
Hi,
On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld <
a.mecklenf...@tu-braunschweig.de> wrote:
> Hello Mark,
>
> thanks for the reply. The point is, I don't.
Ah, I read your original email more closely now. The use of a subject line
that reflected your error message rather than your intenti
Hi,
Thank you Joao, Justin and Marlon for your answers.
Joao, I have been looking at your article the last days as it explains very
well what you have done, particularly in the Supplementary info, so
I am very happy that you answered this thread. Would it be possible for me to
look at your spec
Hello Mark,
thanks for the reply. The point is, I don't. I found some Lennard-Jones
parametrization in literature that distinguishes between intra- and
intermolecular (oxygen atom of water) interactions. My intention was
thus to define the specific eps_ij and sigma_ij for the corresponding
at
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