Many thanks for your advice: the problem was really the one that you
indicated.
Thank you also for the unsolicited suggestions: I really appreciate that.
Carlo Guardiani
> On Wed, Dec 10, 2014 at 4:57 AM, Carlo Guardiani <
> carlo.guardiani.dsf.unica.it> wrote:
>
>> Dear Amber Developers,
>> I am running H-REMD simulations of a peptide using the
>> CUDA version of Amber14. I had no problems running the
>> first 100 ns of the simulation, but when I tried to
>> restart it, the run aborted with the error message:
>>
>> | ERROR: I could not understand line 14935
>> 0.0061866 0.2322136 -0.1654300 0.5206336 0.6339461 0.2485021
>>
>
> ​I suspect the real problem is elsewhere in your inpcrd file. Can you
> look
> through and see if there are any ****s in your restart file that would
> indicate overflowing coordinates?
>
> You didn't set iwrap=1, which suggests that this is a strong possibility.
> ​
>
>
>>
>> Since in my system I have 29864 atoms and the restart file
>> shows the coordinates of two atoms per line, line 14935 is
>> the line where the velocities begin (considering also the
>> two lines before the coordinates). The program thus behaves
>> as if it doesn't understabd that it must perform a restart,
>> so I am wondering if there is some special instruction to
>> restart H-REMD.
>>
>> Here is the content of my input file (for example file
>> hremd.mdin.001):
>>
>> H-REMD
>> &cntrl
>> irest=1, ntx=5,
>> nstlim=1250, dt=0.002,
>> ntt=3, gamma_ln=1.0,
>> tempi=300.0, temp0=300.0,
>> ig=578,
>> ntc=2, ntf=2, nscm=1000,
>> ntp=0, ntb=1, cut=8.0,
>> ntpr=1250, ntwx=1250, ntwr=1250,
>> numexchg=40000,
>> /
>>
>
> ​A few unsolicited suggest​ions regarding your input file: set ig=-1
> to
> seed the random generator from the system clock. This ensures that you
> *always* have a different random seed for each replica for each restart.
> If you have the same seed for different replicas and different restarts
> with Langevin dynamics, your trajectories will begin to synchronize (which
> is a bad thing).
>
> Also, set ntxo=2 to write NetCDF restart files -- this is not vulnerable
> to
> the errors you (probably) got above. You should also (always!) set
> ioutfm=1 to write NetCDF trajectories -- they are *much* higher precision
> (full single precision for each coordinate), *much* faster to write, and
> the resulting files are *much* smaller than if you use the standard ASCII
> trajectory files.
>
> For more complicated REMD simulations (e.g., multi-dimensional replica
> exchange), NetCDF restarts and trajectories are actually required.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Dec 10 2014 - 07:30:03 PST
