[gmx-users] negative steps from tpbconv

[Tsjerk Wassenaar]

Hi Jesper,

Using a .cpt file will also work with the modified .tpr file.
Maybe it is also worth considering using the -maxh option to mdrun,
with nsteps in the .mdp file set to -1 (run infinitely). That avoids
the hassle with extensions.

Cheers,

Tsjerk

2011/2/24 Jesper Sørensen <lists at jsx.dk>:
> Hi Xavier,
>
>
>
> That worked, thanks… Would it also work if I just gave the old state.cpt
> file to mdrun?
>
>
>
> Jesper
>
>
>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of XAvier Periole
> Sent: 24. februar 2011 12:19
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] negative steps from tpbconv
>
>
>
>
>
> Hi Jesper,
>
>
>
> This occurs when you ask for a number of steps that exceed the
>
> the size of an integer! I got the same problem recently ...
>
>
>
> The only solution I found was to make a new mdp file where t0
>
> is the old time and asking for the extension you need ... you can
>
> give trr and edr files to grompp so the tpr file is a continuation of
>
> earlier one ...
>
>
>
> XAvier.
>
>
>
> On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote:
>
> Hi,
>
>
>
> I am trying to extend the run time in tpr file to include more steps using
> tpbconv…
>
> This has worked well for a while, but now I get two errors…
>
> One is that it writes “now -2074660000 steps”, which doesn’t make sense –
> why is this number negative…
>
> Also, “You've simulated long enough. Not writing tpr file”
>
>
>
> If I extend the simulation using the –nsteps flag, then it will write the
> tpr file, but still comes up with negative numbers whens starting mdrun with
> the file, which mdrun does not exactly like.
>
>
>
> Output is a s follows:
>
> READING COORDS, VELS AND BOX FROM TRAJECTORY
> ../T305/512DPPC_9728W_305K_625ns.trr...
>
>
>
> trn version: GMX_trn_file (single precision)
>
> Read    trr frame   4166: step 2124660000 time 53116500.000
>
>
>
> Using frame of step 2124660000 time 5.31165e+07
>
> Extending remaining runtime of by 625000 ps (now -2074660000 steps)
>
> You've simulated long enough. Not writing tpr file
>
>
>
> Best regards,
>
> Jesper
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands