Hey everyone...
I need help I would like to know how to calculate the sasa (solvent
accesible surface area). What quantum or statiscal method to calculate done
that?
Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
deisy yurley rodriguez sarmiento wrote:
Hey everyone...
I need help I would like to know how to calculate the sasa (solvent
accesible surface area). What quantum or statiscal method to calculate
done that?
The tool to use is g_sas. It prints a citation to the method used in the SASA
dear Justin,
tanks for your kindness.I would like to follow up what you say,but I want to
have simulation without wraping.
could these command be helpful?
trjconv -s first1ns.tpr -f whatever_trajectory_you_want(xtc after 3ns
simulation).xtc -pbc mol -center -o fit.gro
grompp -f md300.mdp -c fit.
ana johari wrote:
dear Justin,
tanks for your kindness.I would like to follow up what you say,but I
want to have simulation without wraping.
could these command be helpful?
No. A modified trajectory should not be used for further simulation. "Fixing"
periodicity is only useful for visua
Dear David,
I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:
*one single molecule in gas phase*
Energy
Dear,
When I generated bond parameters as following and ran "grompp", then I had
an error messages "No default Angle types"
[ angletypes ]
; i j k functh0 cth ub0 cub
OST CST OST 5 180.25104.0 0.0 0.0
CS SS FE 5
Hi
This is regarding the pull code.. I have followed your tutorial to get the
PMF for distance between 2 atoms using the pull code. I want to know if one
can bring the atoms closer rather than pull them apart? I want to start from
the maximum distance and then bring them closer to check reversibil
Hyunjin Kim wrote:
Dear,
When I generated bond parameters as following and ran "grompp", then I had
an error messages "No default Angle types"
[ angletypes ]
; i j k functh0 cth ub0 cub
OST CST OST 5 180.25104.0 0.0 0.0
CS
Elisabeth wrote:
Dear David,
I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:
To get heat of vaporiza
Sai Pooja wrote:
Hi
This is regarding the pull code.. I have followed your tutorial to get
the PMF for distance between 2 atoms using the pull code. I want to know
if one can bring the atoms closer rather than pull them apart? I want to
Set pull_rate < 0.
start from the maximum distance
Hi,
I am working my way through learning to use g_bar to obtain a PMF curve.
As far as I can see, the input for g_bar can be hundreds of files. Is
there some general way to feed a large number of file names to a program other
than typing them individually on the command line?
Warren Gallin wrote:
Hi,
I am working my way through learning to use g_bar to obtain a PMF curve.
As far as I can see, the input for g_bar can be hundreds of files. Is
there some general way to feed a large number of file names to a program other
than typing them individual
Dear All,
I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in
simple spc water in a dodecahedron box. I could easily walk through till the
NVT equilibration step after which every thing seems so right(after 5
steps with time step of 2fs using V-rescale thermostat the system
e
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