Dear amber user,
Hi, I am Sohag Biswas, from Indian Institute of Technology Hyderabad,
India. I am trying to simulate 1200 DMF molecules by using OPLS-AA
parameters. After 5000 cycle minimization and 400 ps NVT running, I ran 3ns
NPT simulation. But I am not getting the exact density. the density value
is showing 0.7789 which is less than experimental value (0.93). Please
somebody help me to solve this problem. Here I have given my frcmod and
prepi input. Thank you. Yours sincerely.
remark goes here
MASS
o 16.00 0.000
c 12.00 0.000
h5 1.00 0.000
n 14.00 0.000
c3 12.00 0.000
h1 1.00 0.000
BOND
o -c 648.00 1.229
c -h5 319.40 1.100
c -n 478.20 1.335
n -c3 330.60 1.449
c3-h1 335.90 1.090
ANGLE
o -c -h5 53.890 120.5
o -c -n 75.830 122.9
c -n -c3 63.920 121.9
h5-c -n 52.390 116.6
n -c3-h1 49.820 109.3
c3-n -c3 62.130 116.2
h1-c3-h1 39.180 109.5
DIHE
o -c -n -c3 1 2.500 180.0 2.000
c -n -c3-h1 1 0.000 0.000 0.000
h5-c -n -c3 1 2.500 180.0 0.000
c3-n -c3-h1 1 0.000 0.000 2.000
IMPROPER
h5-n -c -o 1.1 180.0 2.0 Using default
value
c -c3-n -c3 1.1 180.0 2.0 Using default
value
NONBON
o 1.7200 0.210
c 1.9360 0.105
h5 1.5556 0.015
n 1.8027 0.170
c3 1.8700 0.060
h1 1.5810 0.030
prepi file 0 0 2
This is a remark line
molecule.res
MOL INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O1 o M 3 2 1 1.540 111.208 -180.000 -0.500000
5 C1 c M 4 3 2 1.243 150.981 -0.000 0.500000
6 H1 h5 E 5 4 3 1.115 121.537 0.000 0.000000
7 N1 n M 5 4 3 1.367 121.866 -180.000 -0.140000
8 C2 c3 3 7 5 4 1.470 121.260 0.000 -0.110000
9 H2 h1 E 8 7 5 1.070 109.457 59.841 0.060000
10 H3 h1 E 8 7 5 1.070 109.495 179.886 0.060000
11 H4 h1 E 8 7 5 1.070 109.404 -60.124 0.060000
12 C3 c3 M 7 5 4 1.470 121.879 180.000 -0.110000
13 H5 h1 E 12 7 5 1.070 109.456 120.341 0.060000
14 H6 h1 E 12 7 5 1.070 109.454 -119.665 0.060000
15 H7 h1 E 12 7 5 1.071 109.437 0.340 0.060000
LOOP
IMPROPER
H1 N1 C1 O1
C3 C2 N1 C1
DONE
STOP
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Received on Sat Dec 07 2013 - 09:00:02 PST
