[gmx-users] question about solvating

Mark Abraham mark.abraham at anu.edu.au
Thu Jul 8 07:47:19 CEST 2010

Please start new emails for new discussion topics. That way you increase the chance that people with the interest and expertise can use their time efficiently, and that you get an answer. Also, archives work better if you separate topics.

> Please Let me ask two more simple questions about solvating a molecule. I am using genbox to solvate a solute. I have solute.gro and solvent.gro. What should be the dimension of box in solvent.gro if i want to put -nmol numbers in the solute box. Does it matter what size the box of solvent is (last line in gro)?

I don't think you are using the right tool for your problem, but your description is so opaque it's hard to tell. genbox -nmol will try to fill interstices, which need to exist for it to do any good. That means you need to have prepared your solvent.gro with your solute in mind.
> I have solvated the solute with 50 moleecules of solvent. I have the structure file obtained from genbox. To run em or MD I need to have top file. so I am using pdb2gmx and I get a top file for the solute and 50 solvents but I have one moleculetype (named protein by default). I am confused If I need to have 2 molecuels types for solute and solvent, also if I need to enter the number of solvent molecules at the end of the top file [mols] option, or what I have now is fine and I can proceed to em and md usuing mdp files? :)

 1. use pdb2gmx on an unsolvated .gro to get your protein .top
2. use editconf to set the simulation box how you want it
3. use genbox -p to add solvent and take care of modifying your .top (unless your solvent is not water, in which case you'll probably have to do some manual editing of your .top)
4. grompp and mdrun

Perhaps doing some tutorial material will make this and other workflows more readily understood?


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