[gmx-users] Running Lyz in water

[Mark Abraham]

On 06/29/2011 04:18 PM, Ravi Kumar Venkatraman wrote:
> Dear all,
>             I have been running lyz in water. I have 20 ps 
> pre-equilibrated NVT and 200 ps NPT configuration of spce216 water. I 
> am following the instruction from gromacs tutorial. This is the link 
> for the tutorial,
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
>
> After editing the box for lyz and then I tried to solvate the box with 
> spce216 water. I followed the same instruction but it shows fatal I/O 
> error - topol.top. 

That will usually mean you've followed the instructions incompletely. 
However, we don't know what you actually did do, so we can't help other 
than to suggest you go back and try afresh.

> It was not able to find the input file topol.top. But in this tutorial 
> its an output command. Further it shows 6091 solvent instead of 10832 
> as per tutorial. Pls help me find the problem.

Something must be greatly different, and unless Justin's made an error 
in his tutorial and you're the first to notice, it will be something 
you've done.

Mark

>
>
> Thank you
>
> *With Regards,**
> *
> *
> *
> *Ravi Kumar Venkatraman,*
> *c/o Prof. Siva Umapathy,**
> *
> *IPC Dept., IISc.,*
> *Bangalore, INDIA.*
> *Phone No: +91-9686933963*
>

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