[gmx-users] Extending Simnulation - how analyze?

[Andrea Spinelli]

@Mark
The .log report works for 2000 ps.

@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
>>> 
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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.