Hi Vinicius,
Sorry, my last email should have been clearer. I have tried the experiment you suggested, and unfortunately the imin=5 calculation still does not work.
I have attached the results - again it works fine for AMBER14 but not for AMBER16. Can anyone report successfully running imin=5 with AMBER16? Am I the only person using this functionality? :-)
Thanks,
Paul
-----Original Message-----
From: Cruzeiro,Vinicius Wilian D [mailto:vwcruzeiro.ufl.edu]
Sent: 29 November 2017 17:05
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] imin=5 not working in AMBER16?
Hello Paul,
On AMBER16 the default trajectory format changed to binary NetCDF (ioutfm=1). Please try to run both the regular dynamics and the imin=5 calculation with ioutfm=1 and let us know if it works.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Paul Mortenson <Paul.Mortenson.astx.com>
Sent: Wednesday, November 29, 2017 10:51:25 AM
To: AMBER Mailing List
Subject: Re: [AMBER] imin=5 not working in AMBER16?
Hello Vinicius,
The mdcrd file (in ASCII trajectory format) was generated with AMBER16. I have just tried generating a netcdf trajectory and re-running the imin=5 using ioutfm=1, and I get the same error.
The manual (p316-7) seems to suggest that ASCII format is expected by default? I am explicitly setting ioutfm=0 for the imin=5 run.
Thanks,
Paul
-----Original Message-----
From: Cruzeiro,Vinicius Wilian D [mailto:vwcruzeiro.ufl.edu]
Sent: 29 November 2017 15:27
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] imin=5 not working in AMBER16?
Hello Paul,
Did you generate your mdcrd file with AMBER14 or AMBER16? If on AMBER14, did you try using ioutfm = 1?
Regards,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Paul Mortenson <Paul.Mortenson.astx.com>
Sent: Wednesday, November 29, 2017 10:19:37 AM
To: AMBER Mailing List
Subject: [AMBER] imin=5 not working in AMBER16?
Hi,
I'm having trouble getting sander to work with imin=5 (post-processing trajectory files). I have attached a simple test case which works fine for AMBER14, but not with AMBER16.
Sander crashes before outputting any energies, with the following error message:
sander: posixio.c:232: px_pgout: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed.
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x7F29152256F7
#1 0x7F2915225D3E
#2 0x7F291472A26F
#3 0x7F291472A1F7
#4 0x7F291472B8E7
#5 0x7F2914723265
#6 0x7F2914723311
#7 0xA1E92C in px_pgout at posixio.c:?
#8 0xA1F4F6 in px_get at posixio.c:?
#9 0xA1F6FD in ncio_px_get at posixio.c:?
#10 0xA18137 in ncio_get
#11 0xA21D67 in putNCvx_char_char at putget.c:?
#12 0xA29DE5 in writeNCv at putget.c:?
#13 0xA2ABA4 in NC3_put_vara
#14 0xA12A26 in NC_put_vara at dvarput.c:?
#15 0xA12F61 in NCDEFAULT_put_vars
#16 0xA13A56 in NC_put_vars at dvarput.c:?
#17 0xA14902 in nc_put_vars_text
#18 0xA0B414 in nf_put_vars_text_
#19 0xA01829 in __netcdf_MOD_nf90_put_var_1d_text
#20 0x68DB6B in __ambernetcdf_mod_MOD_nc_create
#21 0x691F41 in __binrestart_MOD_write_nc_restart
#22 0x544B4B in master.0.minrit_.part.0.constprop.1 at minrit.F90:?
#23 0x4EEB9A in runmin_
#24 0x4DA2F4 in __trajenemod_MOD_trajene
#25 0x4D83E3 in sander_
#26 0x4CE738 in MAIN__ at multisander.F90:?
Does anyone have any suggestions?
Thanks,
Paul Mortenson
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Received on Thu Nov 30 2017 - 00:00:03 PST
