[gmx-users] negative steps from tpbconv

[Tsjerk Wassenaar]

Hi,

The .cpt defines the state, not the number of steps to go for.

Setting nsteps to -1 should work for the new (>4.5 definitely, >4.0
I'm not sure) versions of gromacs. I think it was introduced right
after the -maxh option was.

@Xavier: I added a number of editing options to tpbconv (4.5.1), among
which the possibility to set the number of steps directly (which can
then be set to -1). You can take the source code from
/data_new3/tsjerk/GMX/gromacs-4.5.1-rtc/src/kernel/tpbconv.c

Groetjes,

Tsjerk

On Thu, Feb 24, 2011 at 1:35 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> 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 <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
>> --
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>
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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