Dear Users,
It is known that electric dipole moment of a water monomer is
experimentally 1.85 D and using the TIP3P model it's supposed to be 2.35D.
I am using the TIP3P model for a water-based simulation in Gromacs 5.1.5.
After applying sinusoidal electric fields in the Y axis, the norm of the
dip
Dear all,
I am applying an electric field to water and I need to calculate its
viscosity at different simulation temperature. I have come across gmx
energy -vis option that outputs shear and bulk viscosity. And another way
is to use gmx tcaf -ov and then apply correction. Since I do not have an
ac
That makes sense.
Thanks a lot, lot for your help.
On Mon, 9 Jul 2018, 00:40 Justin Lemkul, wrote:
>
>
> On 7/8/18 2:37 PM, Sabreen Farnaz wrote:
> > I had read this part from gmx help traj "plots temperature of each group,
> > provides velocities are present...n
ote:
> Hi,
>
> gmx help traj has a useful point to make about how it estimates temperature
> from the velocities.
>
> Mark
>
> On Sun, Jul 8, 2018 at 8:22 PM Sabreen Farnaz
> wrote:
>
> > Thank you, Dr. Lemkul. I have done this but used gmx energy to find the
>
found
different values for the same energy group using them.
On Mon, 9 Jul 2018, 00:10 Justin Lemkul, wrote:
>
>
> On 7/6/18 4:30 PM, Sabreen Farnaz wrote:
> > Dear Dr. Lemkul,
> > Thank you for your answer. Can you please also advise how can I get the
> > temperature o
information.
Regards,
Neelima S.
On Sat, 7 Jul 2018, 00:01 Justin Lemkul, wrote:
>
>
> On 7/6/18 1:07 PM, Sabreen Farnaz wrote:
> > Dear all,
> > This is in regard to my previous queries. The warning in NVT step can
> > possibly be ignored using -maxwarn but I am still not sur
Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the rest!
Can someone please help?
Thanks,
Neelima S.
On Fri, 6 Jul 2018, 01:56 Sabreen Farnaz, wrote:
> Dear all,
>
> I am setting up a sys
Dear all,
How can I get the temperature of a system as a function of distance using
gromacs 5.1.5? gmx energy plots the temperature of the centre of mass of
energy groups against time. gmx traj also does the same from velocity
information.
Please help!
Regards,
Neelima S.
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Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at say
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermost
Dear all,
Currently I am using GPU acceleration to run Gromacs V5.1.5. Energy groups
are still not created for V5.1.5, similar to previous versions, with the
message "NOTE: With GPUs, reporting energy group contributions is not
supported". My question is if this is supported in more recent version
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