[gmx-users] negative steps from tpbconv

[Jesper Sørensen]

Using the cpt file didn't work for me - it remembered the nsteps and quit
before even running anything.
Without getting into the details, I am changing the temperature along the
way in my simulation and therefore I can't use nsteps -1 either.
But Xavier's first suggestion worked, so I will continue using that
solution...

Thanks,
Jesper

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of XAvier Periole
Sent: 24. februar 2011 13:35
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] negative steps from tpbconv


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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