[gmx-users] Re: genbox problem with micelle

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 5 04:03:17 CEST 2007

Alif M Latif wrote:
> Dear GROMACS users and developers,
> I've done 1 ns 
> simulation before this, and the water seems to remain in the micelle 
> structure. I'm using a single workstation with Pentium D, 3.0 GHz, and 
> 2Gb of RAM, so I can't manage to get 0.5-1 ns per day.

Yeah, a nanosecond is nothing :-O

> About the vdwradii.dat that you all said, I'll try to do it. But i'm a 
> beginner in this field (I'm a chemist)..It will take time. By the way, I 
> just thought using Packmol to initially arrange the water to be outside 
> the sphere. So I don't have to use genbox. Can I do that?

Don't know... please consult the packmol documentation :-) It's 
off-topic here. So long as the structure file you give to pdb2gmx uses 
residue names it can recognise as water, you should be OK.


More information about the gromacs.org_gmx-users mailing list