[gmx-users] Extending Simnulation - how analyze?

[V.V.Chaban]

>
> @Chaban
> I not use grompp and the extension not create .trr files.
>
> What I have to do?



- Learn politeness.







>
> 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.
>