[gmx-users] Extending Simnulation - how analyze?

[Andrea Spinelli]

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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>> 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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Andrea Spinelli

Please do not print this email unless really need to.
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