[gmx-developers] how to extend a run using tpbconv?

[Berk Hess]

Hi,

I have fixed problems like this a few weeks ago.
Is this with the newest CVS code?

If not could you try it with the newest code.
If it still you can mail me your new tpr file and your cpt file.

Berk

spitaleri.andrea at hsr.it wrote:
> Hi Berk,
> thanks for your reply. I followed your suggestion but I did not work.
> Basically:
> 1. tpbconv -s old -extend (or until) -o new -> it does not work (it ask
> for trr)
>
> 2. tpbconv -s old -nsteps -o new 
> 2a. mdrun -s new -cpi file.cpt 
> it crashes with this error:
>
> Program mdrun, VERSION 4.0_beta1
> Source code file: domdec.c, line: 5627
>
> Fatal error:
> The size of the domain decomposition grid (12) does not match the number
> of nodes (24). The total number of nodes is
>  24
>
> The only way to get to work it is in the old fashion:
> tpbconv -s -extend -o new -f -e
> mdrun -s new (without file.cpt)
>
> I am just wondering wheter the last procedure is still correct.
>
> Thanks in advance
>
> andrea
>
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute 
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> Tel: 0039-0226434348/5622/3497/4922
> Fax: 0039-0226434153
>
> ----- Original Message -----
> From: Berk Hess <hessb at mpip-mainz.mpg.de>
> Date: Tuesday, September 16, 2008 5:00 pm
> Subject: Re: [gmx-developers] how to extend a run using tpbconv?
>
>   
>> Hi,
>>
>> Extending is only required if you want more steps then you 
>> initially set 
>> in your mdp file.
>>
>> The procedure is to first modify only nsteps in your tpr file and 
>> then 
>> continue from the checkpoint file:
>> 1 tpbconv -s old -extend (or -until or -nsteps) -o new
>> 2 mdrun -s new -cpi file.cpt
>>
>> Berk
>>
>> andrea spitaleri wrote:
>>     
>>> Hi then,
>>> I see that now gromacs can read checkpoint file. Which is now 
>>>       
>> the 
>>     
>>> right procedure to extend a simulation using tpbconv?
>>>
>>> 1. tpbconv -s file.tpr -f file.cpt -extend 1000 -o new
>>> or
>>> 1. tpbconv -s file.tpr -f file.trr -extend 1000 -o new
>>>
>>> 2. mdrun -s new
>>> or
>>> 2. mdrun -s new -cpi file.cpt
>>>
>>> Then, do I need to keep the same number of cpus of the previous 
>>>       
>> run or 
>>     
>>> I can change?
>>>
>>> thanks in advance
>>>
>>> Regards,
>>>
>>> andrea
>>>
>>>       
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