Hello amber:
Im trying to run a FEP calculation, and after 130ps of simulation, I get lots
of warnings (WARNING: vlimit exceeded for step 273242; vmax = 23.94).
Previously to the fep I ran a 1000ps long simulation at the same conditions
(tip3 water, 298K, constant pressure) for equilibrating the system and I had
no one of such wanings. I'm suspicious about the dummy atoms...
I have several dummy atoms and I'm not sure which of the parameters for the
dummies should be 0. In the tutorial (val-to-ala) it seems they use arbitrary
non-zero parameters for everything except the NONB. Coud anybody tell me how
I can have more information about parameters for dummy atoms in FEP's?
Thank you,
Miguel.
---------------------Here is the input file-----------------------
&cntrl
timlim=9999999, nstlim=-1,
ntx=7,
ntpr=20000, ntwx=1000,
ntb=2, ntp=1,
scee=1.2,
ntc=1, ntf=1,
dt=0.0005, vlimit=20.0,
temp0= 298.0, tautp =0.1,
pres0=1.0, taup=0.4,
almdel=0.01, isldyn=-3,
nstmeq=10000, nstmul=10000,
ndmpmc=10,
&end
-----------------------Here are the parameters I used for dummies--------
MASS
d3 1.000 0.000
d2 1.000 0.000
do 16.000 0.000
BOND
c -d3 100.00 1.000
os-d2 100.00 1.000
c3-do 100.00 1.260
ANGLE
ca-c -d3 100.000 109.500
n -c -d3 100.000 109.500
d3-c -d3 100.000 109.500
o -c -d3 100.000 54.750
c -os-d2 100.000 120.000
c3-os-d2 100.000 120.000
ca-c3-do 100.000 120.000
os-c3-do 100.000 120.000
h1-c3-do 100.000 54.750
DIHE
d2-os-c3-c3 1 0.0 0. 2.
hn-n-c3-c3 1 0.0 0. 3.
h1-c3-os-d2 1 0.0 0. 2.
d3-c-n-hn 1 0.0 0. 3.
h1-c3-os-c3 1 0.0 0. 2.
d3-c-n-c3 1 0.0 0. 3.
n-c3-c3-h1 1 0.0 0. 1.
os-c3-c3-h1 1 0.0 0. 3.
n-c3-c3-os 1 0.0 0. 2.
do-c3-os-d2 1 0.0 0. 1.
do-c3-os-d2 1 0.0 0. 2.
o-c-n-hn 1 0.0 0. 3.
do-c3-os-c3 1 0.0 0. 2.
o-c-n-c3 1 0.0 0. 3.
c3-os-c3-h1 1 0.0 0. 2.
c-n-c3-h1 1 0.0 0. 3.
c3-os-c3-c3 1 0.0 0. 1.
c-n-c3-c3 1 0.0 0. 2.
c3-os-c3-c3 1 0.0 0. 4.
ca-c3-os-d2 1 0.0 0. 2.
ca-c-n-hn 1 0.0 0. 3.
ca-c3-os-c3 1 0.0 0. 2.
ca-c-n-c3 1 0.0 0. 3.
hn-n-c3-c3 1 0.0 0. 2.
d2-os-c3-c3 1 0.0 0. 3.
d3-c-n-hn 1 0.0 0. 2.
h1-c3-os-d2 1 0.0 0. 3.
d3-c-n-c3 1 0.0 0. 2.
h1-c3-os-c3 1 0.0 0. 3.
d3-c-n-hn 1 0.0 0. 2.
h1-c3-os-d2 1 0.0 0. 3.
d3-c-n-c3 1 0.0 0. 2.
h1-c3-os-c3 1 0.0 0. 3.
os-c3-c3-h1 1 0.0 0. 1.
n-c3-c3-h1 1 0.0 0. 3.
os-c3-c3-h1 1 0.0 0. 1.
n-c3-c3-h1 1 0.0 0. 3.
n-c3-c3-os 1 0.0 0. 3.
o-c-n-hn 1 0.0 0. 1.
o-c-n-hn 1 0.0 0. 2.
do-c3-os-d2 1 0.0 0. 3.
o-c-n-c3 1 0.0 0. 2.
do-c3-os-c3 1 0.0 0. 3.
c-n-c3-h1 1 0.0 0. 2.
c3-os-c3-h1 1 0.0 0. 3.
c-n-c3-h1 1 0.0 0. 2.
c3-os-c3-h1 1 0.0 0. 3.
c-n-c3-c3 1 0.0 0. 1.
c3-os-c3-c3 1 0.0 0. 2.
c-n-c3-c3 1 0.0 0. 4.
ca-c-n-hn 1 0.0 0. 2.
ca-c3-os-d2 1 0.0 0. 3.
ca-c-n-c3 1 0.0 0. 2.
ca-c3-os-c3 1 0.0 0. 3.
hn-n-c3-h1 1 0.0 0. 3.
hn-n-c3-h1 1 0.0 0. 2.
IMPROPER
d2-c3-os-c3 0.0 0. 2.
do-os-c3-h1 0.0 0. 2.
do-os-c3-ca 0.0 0. 2.
do-h1-c3-h1 0.0 0. 2.
do-h1-c3-ca 0.0 0. 2.
ca-c-ca-ca 0.0 0. 2.
NONBON
d2 0.0000 0.0000
d3 0.0000 0.0000
do 0.0000 0.0000
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Received on Mon Mar 01 2004 - 16:53:00 PST
