Thanks for the response.
Yes, I am sure that I am using ntb = 0. I also know that it works prior to
adding ions, so adding ions is what breaks it.
Interestingly, the last two lines of the inpcrd of the protein only system
reads
82.4450000 14.3940000 -13.6870000 81.7180000 15.3700000 -13.4430000
83.6048830 14.5521392 -13.3126966
whereas the inpcrd with ions reads
86.3470000 12.2630000 -15.2900000 87.2459461 11.6555756 -15.3950273
86.5023142 13.2275008 -15.7734415 86.1831237 12.5406017 -13.8148107
87.2007
This does not look correct to me. But it is purely generated by leap.
Why are there 6 columns in the first place? I'd expect 3 columns *
numberOfAtoms rows. Forgive my gromacs inclination, is this the amber way?
(CRD spec states FORMAT(6F12.7), which is again cryptic to me.)
And in the last one, there is a row with a single column. Is this supposed
to happen?
Regards,
Murat
Here is the full(ish) output including the error. :
Here is the input file:
simple uncostrained minimization
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 0,
ntr = 0,
cut = 10.0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
At line 842 of file ew_box.F90 (unit = 9, file = 'inpcrd')
Fortran runtime error: End of file
On Tue, May 13, 2014 at 11:28 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, May 13, 2014, MURAT OZTURK wrote:
> >
> > I have some experience with gromacs and lammps, but we just got some new
> > GPUs and decided to give amber a try to see how it performs.
>
> What you report works fine for me. I don't think Ilya's comment is
> correct,
> at least if I understand it properly.
>
> Are you *sure* you had the exact same input for the run with ions. In
> particular, check you input and output to look for the value of ntb.
> The default is "1", and if you forgot to explcitly set ntb to 0 in your
> second
> run (with ions), you would get something like the error you report.
>
> ...dac
>
>
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Received on Tue May 13 2014 - 14:00:07 PDT
