Nicu wrote:
Dear all,
I try to match a Martini angle potential (g96) for a CG HD with a
tabulated one. All the other tabulated potentials that I constructed
for bonds and nonbonded work fine. But for angle it does not go
well (the entropy drops from 176 to 100). I put bellow the PYTHON
script that computes the values for this potential and the definition
of HD angle potential in Martini. Do I do a stupid mistake? Or is
something else. I use gromacs 4.0.2. Attached also a fragment of the
angle tabulated potential (table_a1.xvg)
HD ....
[angles]
; i j k funct angle force.c.
1 2 3 2 180.0 25.0
2 3 4 2 180.0 25.0
PYTHON SCRIPT
potential = []
r = 0
value = 0
for i in range(4000):
if r > 0.001:
array = [ 0, 0]
value = 0.5*25*(math.pow((math.cos(r)- math.cos(180)),
2 ))
print r , value
r = r + 0.045
minnu vijayan wrote:
hello friends
for doing normal mode analysis i am trying to create .mtx file .but
in output i am not getting thi .mtx file..what all precautions i have
to take
with thanks
------------------------------------------------------------------------
0.045 31.8979910216 500.0
0.09 31.7769022926 3.57911403889
0.135 31.5758707581 5.34263731333
0.18 31.2960649344 7.07513304778
0.225 30.9391087838 8.76661186444
0.27 30.5070698666 10.4073834889
0.315 30.0024442698 11.9881270889
0.36 29.4281384286 13.4999587078
0.405 28.7874479861 14.9344952478
0.45 28.0840338563 16.2839145311
0.495 27.3218956783 17.5410109444
0.54 26.5053428713 18.6992462311
0.585 25.6389635175 19.7527950567
0.63 24.7275913162 20.6965849744
0.675 23.7762708698 21.5263304878
0.72 22.7902215723 22.2385609456
0.765 21.7748003847 22.8306420678
0.81 20.7354637862 23.3007909289
0.855 19.6777292011 23.6480842933
0.9 18.6071361998 23.8724602578
0.945 17.5292077779 23.9747131822
0.99 16.4494120134 23.9564819756
1.035 15.3731244001 23.8202318322
1.08 14.3055911485 23.5692295933
1.125 13.2518937367 23.2075129144
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