System not equilibrated (NVT or NPT) in GROMACS 2018.2& 2021.5

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1

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GROMACS modification: Yes/No
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I need to run MD simulation for PEG(292-mers) in explicit water using GROMACS packages. I have minimized the system and got the .gro file copy the end of log file blew:
Steepest Descents converged to Fmax < 1000 in 229 steps
Potential Energy = -1.2892695e+06
Maximum force = 4.9211905e+02 on atom 2040
Norm of force = 5.7708789e+01

When I tried to equilibrate it (NVT or NPT). It started with a very high temperature and pressure and not completed. I run the same PEG but with different repeat unit (4,upto 250-mer) and run fine but when I got to this one I got problem with the equilibration. I used mdp file from Gromacs protein tutorial. Any suggestion how to equilibrate the system.

Many Thanks,
Amnah

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Any idea?

3

Sorry, I forgot to show the starting nvt stp before collapse. I copied it below:

There are: 88000 Atoms

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
RMS relative constraint deviation after constraining: 3.37e-06
Initial temperature: 297.824 K

Started mdrun on rank 0 Fri Jun 17 10:51:15 2022

       Step           Time
          0        0.00000

Energies (kJ/mol)
Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14
1.26818e+02 1.57570e+03 1.56443e+03 1.16000e+05 1.10395e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest.
1.82844e+05 -1.04000e+04 -1.49758e+06 6.04784e+03 3.56727e+00
Potential Kinetic En. Total Energy Conserved En. Temperature
-1.18877e+06 1.02124e+08 1.00935e+08 1.00935e+08 1.38886e+05
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.96275e+02 1.28795e+06 8.12593e+00

4

Hi,
Did you check the starting structure to verify that all the molecules can be accommodated properly in the box? Since you had no problem with shorter chain, I am guessing that it can be some issue in the initial structure.
\Alessandra

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Thanks alevilla for the reply,
Yes, I think you are right. I will try to increase the size of the box, so the all atom can be accommodated in the box and see

Best