Dear Gromacs Users,
I was just wondering if the formula and the units which I use for getting the
entropy is absolutely correct.
The eigenfrequency (v) in cm-1 are obtained from eigenfreq.xvg.( GMX ver 4.0.7,
using normal mode calculations)
TS = [alpha/exp(alpha)-1] - log[1-exp(-alpha)]
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sreelakshmi ramesh wrote:
Dear all,
i am trying to simulate a double walled cnt in tip4p
water using oplsaa force field.
first i used
*g_x2top -f carbon.pdb -o carbon.top* ( successfully created the topology)
* editconf -f carbon.pdb -o carbon_newbox.gro -c
sreelakshmi ramesh wrote:
Dear all,
when i run energy minimization i get the following error.
the topology file was created from the starting pdb file using g_x2top
*grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3*
In general, the use of -maxwarn is
I have patched g_order version 4.5.4 to compute the order parameters
in a different way. Despite trying, I don't understand the original
g_order implementation. In the version that I am providing, the
hydrogens are explicitly built and the coordinates of these hydrogens
are output to
You can calculate that by hand on a calculator in a few seconds.
There is no need to use Gromacs.
On Jun 10, 2011, at 2:27 PM, Nilesh Dhumal wrote:
Hello,
How can I calculate Lennard Jones interaction for two selected
atoms with
a specific distance?
I am using Gromacs 4.0.7 version.
If eplilon of hydrogen atom is zero then the lennard jones interaction of
OH bond (at 0.22nm)is also zero.
Is it correct?
I used equation 4.5 to calculate LJ energy.
Nilesh
On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
How can I calculate Lennard
The LJ interaction is 0. But you're asking about a bond. 1-2
interactions are typically modeled with a harmonic potential. This is
most definitely not zero.
On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote:
If eplilon of hydrogen atom is zero then the lennard jones
interaction of
OH
Basically I want to calculate LJ interaction for OH bond.
If I use eq. 4.5 in manual to calculate LJ interaction then zero.
How can I calculate LJ interaction of a bond?
Nilesh
On Fri, June 10, 2011 3:00 pm, Andrew Paluch wrote:
The LJ interaction is 0. But you're asking about a bond. 1-2
Nilesh Dhumal wrote:
Basically I want to calculate LJ interaction for OH bond.
If I use eq. 4.5 in manual to calculate LJ interaction then zero.
How can I calculate LJ interaction of a bond?
This type of measurement doesn't make any sense. Bonded interactions up to 3
bonds away are
I get this error when trying to http://www.gromacs.org/*
Site settings could not be loaded
We were unable to locate the API to request site settings. Please see below for
debugging information. If this is a new install, try refreshing - the API is
simply taking its time loading up!
HTTP
Dear Gromacs Users,
My file has no problem when i grompp with verison of 4.0.7
When i swith to Gromacs 4.5.3 and grompp my file, it gives this reports:
NOTE 3 [file grompp.mdp]:
You are using a plain Coulomb cut-off, which
Dear justin., Thank you tfor your reply
Can i combine Simulated annealing protocol with SMD . if
possible what Time factor should i consider to avoid Clashes in Md simulation
i am asking whether any relation between time of pulling and time of annealing
should i have
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