I had similar problem before. Change the parameter ntwprt. In the input
below it is saving only 22 atoms I think.
On 16 Jun 2016 01:51, "Yeng-Tseng Wang" <c00jsw00.gmail.com> wrote:
> 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 - 10:00:04 PDT
