Minimization step for Gold Nanoparticle

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1

GROMACS version: 2020.4
GROMACS modification: Yes/No
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Dear all,

I am using Gromacs to simulate the interaction between a Gold nanoparticle with a DOPC membrane using the Martini force field. The entire system includes:
DOPC 1568
W 154221
MOL 1
with MOL is the Gold nanoparticle (AuNP) coated with alkyl chains that I defined separately which has a total of 31,369 beads.

Now I am struggling with the minimization step of this system. At first, I used POSRES to make the core of AuNP as a rigid body, however after minization the AuNP was always blown up! So, I used the other command freezegrps to fix it, the AuNP could be stable then but I could see its potential energy still too high! After that I tried to run NVT, the error came as expected:
"
Fatal error:
Step 0: The total potential energy is 7.69995e+11, which is extremely high. The LJ and electrostatic contributions to the energy are 7.61478e+08 and 7.69231e+11, respectively. A very high potential energy can be caused by overlapping interactions in bonded interactions or very large coordinate values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.
"
I am not sure which is the best approach for the minimization step for this system. Could you please give me some suggestions and advice? I do really appreciate it!.

Thank you very much!

Best regards,

Dan

2

Hi,

The error message indicates that you have two or more CG beads to close to each (high repulsion). You need to release the contacts between the CG beads. You can run energy minimization, but without position restrain and other option that “block” bead positions.
You can see which bead are overlapping you can build again your starting structure and try to avoid such overlapping.

In alternative, if you have implemented some force field parameters your self and the starting structure looks reasonable, you can check that the newly implemented parameters are correctly added (e.i. unit ).

Best regards
Alessandra

3

Hi Alevilla,

Thank you very much for your great suggestion! I am going to check the system once again and follow your instruction!

Best regards,

Danh