Hi
There seems to be no problem.
What you tried to open in a text editor is netcdf (binary) format.
I don’t see anything wrong in this unless you are unable to
visualize this in VMD or Chimera.
On Friday, 5 February 2021, Tomasz Miernik <
tomasz.miernik.cm.umk.pl> wrote:
> Hello,
> I'm using, Amber16, AmberTools17, Centos7,CUDA8.0/9.0/9.2.
> Compilation looks good, .out file too:
> -------------------------------------------------------
> Amber 16 PMEMD 2016
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 16
>
> | Run on 11/18/2020 at 11:01:36
>
> | Executable path: /home/obliczenia/amber16/exe/pmemd.cuda
> | Working directory: /home/zadania/miery/T_Amber
> | Hostname: tesla4
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: equil.in
> | MDOUT: equil_1.out
> | INPCRD: density.rst
> | PARM: gsk3b_lig.prmtop
> | RESTRT: equil_1.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: equil_1.mdcrd
> | MDINFO: mdinfo
> | MDFRC: mdfrc
>
>
> Here is the input file:
>
> equil com_4_sol
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=5000000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=500, ntwx=5000, ntwr=5000
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
> BUT
> During the calculations, I get an mdcrd file with the following content:
> CDF^B^.^.^.^B^.^.^.
> ^.^.^.^F^.^.^.^Eframe^.^@^@^@^@^@^@^@^@^@^Gspatial^@^@^@^@^
> C^.^.^.^Datom^.^.�h^@^@^@^Lcell_spatial^@^@^@^C^@^@^@^
> Elabel^.^.^.^.^.^@^E^@^@^@^Lcell_angular^@^@^@^C^@^@^@^L^
> .^.^.^F^.^.^.^Etitle^@^@^@^@^@^@^B^@^@^@^@^@^@^@^Kapplication^@^@^$
> picosecond^@^@^@^@^@^E^@^@^@^D^@^@^@^@^@^@^C^\^@^@^@^
> Gspatial^@^@^@^@^A^@^@^@^A^@^@^@^@^@^@^@^@^@^@^@^B^@^@^@^D^@
> ^.^.^.^.^.^C^D^.^.^.^Kcoordinates^.^.^.^.^C^.^.^.^.
> ^@^@^@^B^@^@^@^A^@^@^@^L^@^@^@^A^@^@^@^Eunits^@^@^@^@^@^@^B^@^@^@^Hangst$
> }B�A~BT�(B ��B�i%BP��B ��B�WmBM�tB
> �EB��uBS��B^E`�B��*BU@�B^B��B�4�BO��B^B^VpB�d�BL^\�B^AB�B��^HBNM�B^D�^PB�
> IBR8jA��=B��2BU��A�MXB��(BS�AA���B�^^}BN��A��^]B�F(BN^^�A�
> �$B��^OBPҪA촴B�d^MBI^\�A�ЙB��BBI�ΙA6^YB�0�BFN(A�ppB���BF��
> A癴^�B���BIMZAᙴ6_B�5DBES�A
> "ϙB�'�BC�|A䙴�.B��OBX��B^H^C^B�9�BY��B^G^B�B��ۙB[_љB^KԼB�ռ弴BZ^A7B^L
> .B�漴鼴B_�MB^O)/B�nмB^��$
> B�,�B^T^.%B�
> }B�)�B^O7�B�~NB���B^XHUB�Y#B���B^[��B^?�^LB�)OB^X>)B}^×B���
> B^T��B��CB|m^ZB^Xu�B��^AB{��B^[�YB~_^FByh�B^X�^DB���B{�8B^T̗
> +B|^DNB�ߗiB^\�]B}��B���B
> ��Bvٗ.B�'^ZB^[9�Bu�VB�a
> B^W�SBr��B�3yB^^�*BtnGB���B!Z^.Bmŗ^GB��VB^[z�Blڗ1B�HDB^X��BiQ^^B�3rB^^̃$
> ^ZBV.^XB`jUB3b"BS��B^��B+^[�BR7�B`��B'�UBQ�
>
> Where is problem ???
> Regards.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
Elvis
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Received on Fri Feb 05 2021 - 17:30:02 PST
