[gmx-users] mdrun rerun to large frame numbers

[Sebastian]

Hi,

On 07/07/2016 12:53 PM, Mark Abraham wrote:
> Hi,
>
> Hmm, that sounds like your very long trajectory is running into some
> integer exceeding its maximum size. mdrun proper uses a 64-bit integer for
> step number, but doubtless there are dusty corners. Are you able to
> estimate which frame number this was?

It seems to be a problem of the step number (around 2e+9) to make the 
trouble.

> What does gmx check say about the
> very long trajectory?

gmx check works fine. Giving all the outputs I am used to like:

Step  500000
Coords 500000 ........................

no trouble.

> To work around it, you can probably just use gmx
> trjconv to break the trajectory into parts, but we'd rather find the
> problem and fix it :-)

I tried this now it always works for the first half but not for the second.
Is there a way to change the step number? Since the frame number does 
not seem to produce the error.

>
> Mark


Thanks,

Basti


>
> On Thu, Jul 7, 2016 at 11:59 AM Sebastian <
> sebastian.buchenberg at physik.uni-freiburg.de> wrote:
>
>> Hey,
>>
>> I try to perform an rerun of very long trajectories using mdrun.
>> The problem is, that the rerun crashes after it reaches a certain frame
>> number with the warning:
>>
>> there may be something wrong with the energy file XXX.edr
>> Found: step=-1983077269, nre=49, nblock=0, time=4.62378e+06.
>> Trying to skip frame expect a crash though.
>>
>> I tried it for three different runs and I get always the same warning.
>> The step number is something strange.
>>
>> Best,
>>
>> Basti
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