[gmx-users] (no subject)

[Mark Abraham]

jyoung wrote:
> 
> Dear gmx-users
> 
> I'm a novice of GROMACS.

That's fine, but to get effective help you need to construct an 
effective request. See 
http://www.catb.org/~esr/faqs/smart-questions.html for ways to do that 
effectively.

Mark

> I want to simulate for lipid bilayer with antimicrobial peptide.
> 
> I downloaded a lipid pdb from Tielmann's site but I have two questions 
> for MD simulation.
> 
> First.
> How can I solvate peptide with the lipid pdb ?
> Editconf and genbox lead some error.
> I think because the pdb of lipid already formed by box type, but I don't 
> have idea.

Neither do we, because you've told us nothing.

> Two.
> I want to simulate for only lipid using by downloaded pdb.
> So I proceeded step by step and I succeeded in energy minimization step.
> When I run restraints MD, I showd an error message as follows.
> 
> "Check for bad contacts and/or reduce the timestep. ~~~"
> 
> Would you tell me what is wrong?

We can't tell yet.

> I already search gmx_users mailing list but I didn,t hear from list.

Mark