RE: [gmx-users] Limitations of simulations?

2013-07-23 Thread Fábio Filippi Matioli 
I would like to stop to receive this e-mail, how can i procide?Thanks

Fábio Filippi MatioliGraduando em Física MédicaUNESP-BotucatuTel (19) 9291.6738

> Date: Tue, 23 Jul 2013 22:57:29 -0700
> From: jsab...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Limitations of simulations?
> 
> I just finished this tutorial and found it very informative:
> http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
> 
> However, This was based on a complex from a pdb.
> 
> I was wondering if it was possible to just simulate the protein without
> complex and put the ligand as a solute and actually have it complex with
> the protein. Obviously, if it could do this it would take a much longer
> time than just simulating a complex, but if given enough time, could it
> complex?
> 
> I have no formal experience with simulations and currently have no one
> around me with enough knowledge on these topic to mentor me, so any help is
> very much appreciated!
> 
> Thank you! :)
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[gmx-users] Extending simualtions

2013-05-29 Thread Fábio Filippi Matioli 
Hello, I have a problem.
I try to extending my simulation. I made this steps.

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt

I need to put more things on mdrun, or only this? because my first mdrun had 4 
or 5 outputs, or the extending recognize de outputs from the first time?
I cant run, and gromcs give me this error 

File appending requested, but only 2 of the 4 output files are present

Tnks


Fábio Filippi MatioliGraduando em Física MédicaUNESP-BotucatuTel (19) 9291.6738 
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