[gmx-users] pullx.xvg / pullf.xvg

[Poojari, Chetan]

Hi Carsten,

Thank you very much. 

I reran my files:

grompp -f  md_umbrella.mdp  -c conf144.gro  -p topol.top  -n index.ndx  -o 144.tpr

mdrun -s 144.tpr  -rerun umbrella144.xtc  -e 144.edr  -o 144.trr  -pf pullf.xvg  -px pullx.xvg


Output: 144.tpr, 144.trr, 144.edr, pullx.xvg, pullf.xvg.



Kind regards,
chetan.

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Carsten Kutzner [ckutzne at gwdg.de]
Sent: 16 December 2010 14:28
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] pullx.xvg / pullf.xvg

On Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote:

> Hi,
>
> Following were the commands which i used in the umbrella sampling simulations:
>
> grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o umbrella500.tpr
>
> mdrun -v -deffnm umbrella500
>
>
> Output:    umbrella500.xvg, umbrella500.xtc, umbrella500.trr, umbrella500.log, umbrella500.gro, umbrella500.edr, umbrella500.cpt
>
>
> pullf.xvg and pullx.xvg files were not produced.
With -deffnm you specified a default filename for all output files.
Try to use mdrun -pf pullf.xvg -px pullx.xvg -s input.tpr
Adding -h to mdrun will show you how your output files will be called.

Carsten

>
>
> Please can I know should i mention -px  pullx.xvg  and  -pf  pullf.xvg in the mdrun?
>
>
> Kind regards,
> chetan
>
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of chris.neale at utoronto.ca [chris.neale at utoronto.ca]
> Sent: 15 December 2010 17:00
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pullx.xvg / pullf.xvg
>
> please copy and paste your commands your output. It is unlikely that
> any of us are going to do that tutorial in order to understand your
> question.
>
> -- original message --
>
> Hi,
>
> I am following the umbrella sampling tutorial written by Justin Lemkul.
>
> I was successfully able to run the umbrella sampling simulations, but
> for each configuration it outputted a single xvg file.
>
> For the data analysis i should have pullf.xvg / pullx.xvg files....but
> these files are not outputted after the simulation run.
>
> I haven't made any changes to the .mdp files mentioned in the tutorial.
>
>
> Please can i know what might have gone wrong that it has not produced
> pullf.xvg and pullx.xvg files.
>
>
>
> Kind regards,
> chetan.
>
>
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