Dear Ross,
Thanks for your help.
Phil
2016-06-16 0:05 GMT+08:00 Ross Walker <ross.rosswalker.co.uk>:
> Hi Yeng,
>
> You have ntwprt = 22 in you cntrl namelist - this tells pmemd to only
> write atoms 1 to 22 to the MDCRD file. If you want all 157K atoms then
> remove this entry.
>
> All the best
> Ross
>
> > On Jun 15, 2016, at 8:50 AM, 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)
> > .........
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Jun 15 2016 - 09:30:03 PDT
