positive binding energy

[bahare bamdad]

Dear all,

I'd like to calculate the binding energy of a protein to a metal organic framework. I used Gromacs to perform MD simulation. However, I receive a lot of positive interaction energy (please see the attachments). Could you please provide your feedback?

Best regards,

Bahareh

[bahare bamdad]

---------- Forwarded message ---------
From: bahare bamdad <bahare...@gmail.com>
Date: Sun, May 21, 2023 at 10:10 AM
Subject: positive binding energy
To: gmx_MMPBSA <gmx_m...@googlegroups.com>

Dear all,

I just sent an email regarding positive binding energy. Let me explain the issue in greater depth. To calculate the binding energy, use gmx_MMPBSA. I used Gromacs to perform the following MD simulation steps:
1. I manually insert protein into the mof pore.
2. I performed energy minimization and simulated annealing by allowing the system to slowly change from 0 to 298 K.
3. I performed 10 ns NVT and NPT equilibration.
Finally, I perform 10 ns MD production. But I get a positive binding free energy (the experiment results show that this type of protein can enter the MOF, so I expect a negative binding energy between the protein and the MOF). I would appreciate it if you could share your feedback with me so that I can improve the results.
Furthermore, Gromacs MD analysis yields a positive LJ(SH) for the system; however, gmx_MMPBSA yields a negative value for the Van der Waals interaction. Could you please tell me if this makes sense?

Best regards,

Bahareh

[Mario Ernesto]

he reason why you got a positive vdW is because there are atoms too close in your system (see picture)... the protein atoms are clashing with those of the MOF... please, review your input structure 

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[marioe911116]