and Cl, defined as 2 molecule types). Is there a way that I can tell
gromacs to include both molecules insertions in the free energy
calculation? In the documentation, I could only find how to specify 1
molecule for the calculation.
Thank you,
Jo
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Hi,
Is there a way to calculate structure factor in gromacs? From the gmx rdf
function?
Thanks!
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.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040458.html
Can you please direct on what I might be doing wrong?
Thank you,
Jo
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Hello,
I would like to calculate viscosity using the Green-Kubo method. I
understand that the viscosity calculation using g_energy uses the msd
method. Is there any built in command in gromacs for green-kubo? Or would
I need to do that by hand?
Thanks,
Jo
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water, and I
also suspect 'settles' could be causing the lack of energy conservation.
Can anyone provide any suggestions on what I can do to conserve energy? I
have attached the mdp file.
Thank you,
Jo
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suggestions on what I can try or
anything I am wrongly assuming!
verlet-buffer-tolerance = -1
rlist = 1.3
coulombtype = PME
rcoulomb = 1.3
coulomb-modifier = Potential-shift
vdw-type = Cut-off
rvdw = 1.3
vdw-modifier = Potential-shift
Best,
Jo
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Hello,
I would like to calculate bulk and shear viscosity on gromacs using
g_energy. I have read a number of other emails about this topic but there
still seems to be no conclusive answer to how to use this tool. I use the
following command:
gmx energy -f prod_500.edr -vis viscosity.xvg
10 ns and I saved energies every 1 ps but the
>>>> results were far and the curves go to negative values.
>>>> Please, do have an idea how to get accurate results?
>>>> Thank you
>>>> Ali
>>>>
>>>>
>>> You give no infor
Hello,
I would like to run a simulation where I need to track the position of a
single molecule and determine the amount of time it moves a certain
distance. Is there a way to do this in gromacs?
Thanks!
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that 'settle' has
not been a problem for energy conservation previously.
I have also tried different versions of Gromacs (5.1.4 and 2018), but the
energy shift still occurs.
Can you recommend any other parameters to change? Or any other strategies
to go about conserving energy for NVE?
Best,
Jo
bra...@gmail.com>
wrote:
> Hi,
>
> Thanks - we need some more information to be able to help. What does
> bin/gmx -version report?
>
> Mark
>
> On Wed, Mar 21, 2018, 19:28 Jo <jojo412...@gmail.com> wrote:
>
> > Hello,
> >
> > I have had s
1000
On Mon, Mar 19, 2018 at 5:08 PM, Jo <jojo412...@gmail.com> wrote:
> Hello,
>
> Thank you for your response. I have found a way to conserve energy of my
> box of SPC/E water by removing 'settles' from my topology file.
> Previously, the total energy of the system was co
about constraining the atoms as a rigid water molecule so that
I don't loose energy conservation?
Thank you in advance,
Jo
On Fri, Mar 16, 2018 at 4:51 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
> Hi,
>
> On Fri, Mar 16, 2018 at 7:42 PM Jo <jojo412...@gmail.com> w
'
failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:546: recipe for target 'check' failed
make: *** [check] Error 2
Thanks,
Jo
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rom the paper
<https://www.biorxiv.org/content/biorxiv/early/2016/10/24/083055.full.pdf>Mark
referenced)?
Thank you!
On Tue, Mar 20, 2018 at 1:39 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
> Hi,
>
> On Mon, Mar 19, 2018 at 10:08 PM Jo <jojo412...@gm
my coulombic cutoff?
Would appreciate any input on these questions!
Best,
Jo
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit= 0
dt = 0.0005
nsteps = 100
; For exact run continuation
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