[gmx-users] Extending Simnulation - how analyze?

Wed Jul 15 15:03:49 CEST 2015

Yes!!
It works very good!!
Thank you, Mark!!

On Jul 14, 2015, at 11:39 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
> 
> Was that actually your mdrun command line? I think you need
> 
> gmx mdrun -s md_0_2 -deffnm md_0_1 -cpi md_0_1 (with or without -append)
> 
> to actually get appending happening. mdrun does not deduce the names of the
> output files from the contents of the checkpoint file.
> 
> Mark
> 
> On Tue, Jul 14, 2015 at 9:47 AM Andrea Spinelli <spinelli87 at gmail.com>
> wrote:
> 
>> Hi Mark,
>> in the .log file there are this lines at the start of the extending.
>> 
>> There are: 20587 Atoms
>> Charge group distribution at step 500000: 5190 5166 5109 5122
>> Initial temperature: 319.123 K
>> 
>> Started mdrun on rank 0 Sun Jul 12 20:50:29 2015
>>           Step           Time         Lambda
>>         500000     1000.00000        0.00000
>> 
>> 
>> 
>> On Jul 14, 2015, at 9:32 AM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>> 
>>> Hi,
>>> 
>>> On Tue, Jul 14, 2015 at 8:10 AM Andrea Spinelli <spinelli87 at gmail.com>
>>> wrote:
>>> 
>>>> @Mark
>>>> The .log report works for 2000 ps.
>>>> 
>>> 
>>> Sure, but you need to look at the bit between 1 ns and 2 ns to find out
>>> what happened when you attempted to append.
>>> 
>>> Mark
>>> 
>>> 
>>>> @Chaban
>>>> I not use grompp and the extension not create .trr files.
>>>> 
>>>> What I have to do?
>>>> 
>>>> On Jul 14, 2015, at 3:56 AM, V.V.Chaban <vvchaban at gmail.com> wrote:
>>>> 
>>>>> The no-headache route is:
>>>>> 
>>>>> mv confout.gro conf.gro
>>>>> grompp
>>>>> mdrun
>>>>> trjcat -f *.trr -o fixed.trr
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Mon, Jul 13, 2015 at 6:45 PM, Mark Abraham <
>> mark.j.abraham at gmail.com>
>>>> wrote:
>>>>>> Hi,
>>>>>> 
>>>>>> What did the .log file report about your attempt to append?
>>>>>> 
>>>>>> Mark
>>>>>> 
>>>>>> On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli <
>> spinelli87 at gmail.com>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> I’m new user of Gromacs and I need extend a simulation of 1000ps.
>>>>>>> On Gromacs 5.0.5 I use this command line as tutorial said.
>>>>>>> 
>>>>>>> gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
>>>>>>> gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append
>>>>>>> 
>>>>>>> It produced the md_0_2.tpr , but when I run rms command to watch the
>>>> state
>>>>>>> of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why?
>>>>>>> What is the command I have to use?
>>>>>>> 
>>>>>>> to view rmds I use this command line:
>>>>>>> gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg
>>>>>>> 
>>>>>>> Thanks a lot.
>>>>>>> 
>>>>>>> 
>>>>>>> Andrea Spinelli
>>>>>>> 
>>>>>>> Please do not print this email unless really need to.
>>>>>>> Save paper, save trees, save space, save money - life matters.
>>>>>>> 
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>>>> 
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Andrea Spinelli

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