Dear all,
I fellow the website (
http://gamd.ucsd.edu/installation.html) to install
GaMD with amber14. Then I run a GaMD simulations, but the trajectory file
is wrong. I checked the trajectory file and the atom numbers of
trajectory file doesn't match the top file. Could you tell me how to
overcome the bug?
Kindly regards,
Phil
*INPUT:*
GAMD for Mu/cell mem
&cntrl
imin = 0, irest = 0, ntx = 1,
nstlim = 50000000, dt = 0.002,
ntc = 2, ntf = 2, tol = 0.000001,
iwrap = 1, ntb = 1, cut = 8.0,
ntt = 3, temp0 = 310.0, tempi = 310.0,
ntpr = 500000, ntwx = 5000, ntwr = 500,
ntxo = 1, ig = -1, ntwprt = 22,
igamd = 3, iE = 1, irest_gamd = 0,
ntcmd = 2000, nteb = 2000, ntave = 1000,
sigma0P = 6.0, sigma0D = 6.0,
/
*trajectory file:*
default_name
68.523 41.212 118.805 68.398 40.528 118.073 68.266 40.810 119.695
69.487
41.492 118.922 67.562 42.335 118.546 67.462 42.616 117.498 66.140
41.901
118.882 65.960 40.982 118.324 66.095 41.502 119.896 65.001 42.902
118.495
65.302 43.908 118.786 64.796 42.955 117.426 63.609 42.589 119.100
63.391
41.563 118.803 63.753 42.671 120.178 62.505 43.340 118.500 62.138
42.909
117.663 61.964 44.429 118.991 62.318 44.916 120.122 63.134 44.525
120.569
62.060 45.865 120.351 61.054 45.037 118.376
110.814 116.262 147.669
67.551 41.271 117.281 67.039 40.546 116.799 67.792 40.879 118.180
68.418
41.471 116.804 66.813 42.554 117.336 66.725 43.116 116.406 65.451
42.208
117.917 65.158 41.165 117.799 65.403 42.382 118.992 64.262 43.081
117.296
64.521 44.124 117.479 64.029 42.992 116.235 63.032 42.729 118.121
62.877
41.661 117.964 63.230 42.867 119.184 61.900 43.570 117.647 61.349
43.132
116.923 61.575 44.768 118.031 62.383 45.429 118.851 63.242 44.996
119.157
62.225 46.410 119.029 60.504 45.325 117.582
110.814 116.262 147.669
.....
*TOP file:*
%VERSION VERSION_STAMP = V0001.000 DATE = 04/19/13 02:55:11
%FLAG TITLE
%FORMAT(20a4)
default_name
%FLAG POINTERS
%FORMAT(10I8)
157191 20 139348 17416 61658 20513 101171 42202 0
0
392835 39367 17416 20513 42202 59 120 68 46
1
0 0 0 0 0 0 0 1 50
0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
.........
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Received on Wed Jun 15 2016 - 09:00:14 PDT
