[gmx-users] (no subject)

[jyoung]

Dear gmx-users

I'm a novice of GROMACS.
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.

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

Thanks.




==================================
Jee-Young Lee, Ph.D
Research Professor
Bio/Molecular Informatics Center
Konkuk University 
C.P.     82-17-348-2107
e-mail. jyounglee at unitel.co.kr
                  jyoung at konkuk.ac.kr
==================================
 

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