I am not sure the use of cpt would work! I might have tried and
got a problem since the cpt might define where it is going (nsteps) ...
to be tried!
@Tsjerk: I have not been able to use the nsteps set to -1 for some
reason it was telling it had ran enough! Any idea why would that be?
On Feb 24, 2011, at 1:01 PM, Tsjerk Wassenaar wrote:
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 <[email protected]>:
Hi Xavier,
That worked, thanks… Would it also work if I just gave the old
state.cpt
file to mdrun?
Jesper
From: [email protected] [mailto:[email protected]
]
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
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