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
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