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标题: 求助：多肽和细菌膜模拟400ns在最后几帧多肽离开膜表面 [打印本页]

作者
Author: boyading 时间: 2025-10-25 16:17
标题: 求助：多肽和细菌膜模拟400ns在最后几帧多肽离开膜表面
在进行多肽与细菌膜的模拟得到了gro和xtc文件，用脚本gmx trjconv -f step7_production.gro -s step7_production.tpr -o md_nowat.gro -n index.ndx -pbc mol

gmx trjconv -f step7_production.xtc -s step7_production.tpr -o md_nowat.xtc -n index.ndx -pbc mol处理之后，发现多肽在最后几帧远离膜而且在膜上下跳动出现，请问是什么原因导致的？

日志是显示最后出现了不稳定的结构吗？

Step Time

199100000 398200.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.60194e+04 8.38595e+04 6.52764e+04 6.34166e+02 -7.57179e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.29845e+04 1.26922e+05 6.01070e+04 -1.50956e+06 5.15665e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13868e+06 2.89993e+05 -8.48682e+05 1.66605e+07 3.03217e+02

Pressure (bar) Constr. rmsd

5.41704e+01 3.63312e-06

Step Time

199200000 398400.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.66507e+04 8.43629e+04 6.49010e+04 6.59376e+02 -4.47590e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.27453e+04 1.27843e+05 6.02020e+04 -1.50864e+06 5.14114e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13618e+06 2.90250e+05 -8.45926e+05 1.66694e+07 3.03486e+02

Pressure (bar) Constr. rmsd

-1.37429e+02 3.63650e-06

Step Time

199300000 398600.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.64092e+04 8.44922e+04 6.47054e+04 7.10945e+02 -7.22261e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.29175e+04 1.26833e+05 5.89707e+04 -1.50688e+06 5.00082e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13692e+06 2.91408e+05 -8.45508e+05 1.66781e+07 3.04696e+02

Pressure (bar) Constr. rmsd

1.01251e+01 3.68815e-06

Writing checkpoint, step 199365400 at Wed Oct 22 14:15:04 2025

Step Time

199400000 398800.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.61779e+04 8.33606e+04 6.53417e+04 6.51282e+02 -7.46108e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.29413e+04 1.27075e+05 6.03576e+04 -1.50855e+06 5.04959e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13767e+06 2.88843e+05 -8.48827e+05 1.66869e+07 3.02015e+02

Pressure (bar) Constr. rmsd

1.74479e+02 3.69328e-06

Step Time

199500000 399000.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.64143e+04 8.40088e+04 6.45304e+04 6.10348e+02 -5.77784e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.27883e+04 1.27868e+05 6.10017e+04 -1.51003e+06 4.94226e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13792e+06 2.90247e+05 -8.47675e+05 1.66958e+07 3.03482e+02

Pressure (bar) Constr. rmsd

8.84313e+01 3.71435e-06

Step Time

199600000 399200.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.58197e+04 8.40882e+04 6.52720e+04 6.47958e+02 -5.28655e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.27638e+04 1.26790e+05 5.97268e+04 -1.50756e+06 4.98318e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13753e+06 2.89795e+05 -8.47730e+05 1.67045e+07 3.03010e+02

Pressure (bar) Constr. rmsd

3.63599e+01 3.72897e-06

Step Time

199700000 399400.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.61669e+04 8.42660e+04 6.51377e+04 7.06687e+02 -5.81579e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.31233e+04 1.27317e+05 5.87602e+04 -1.50618e+06 5.15512e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13561e+06 2.89434e+05 -8.46171e+05 1.67134e+07 3.02633e+02

Pressure (bar) Constr. rmsd

-1.22480e+02 3.65040e-06

Writing checkpoint, step 199781900 at Wed Oct 22 14:30:04 2025

Step Time

199800000 399600.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.62065e+04 8.40609e+04 6.46725e+04 7.01784e+02 -3.96978e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.27491e+04 1.26788e+05 5.81694e+04 -1.50653e+06 5.12706e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13809e+06 2.89419e+05 -8.48674e+05 1.67223e+07 3.02617e+02

Pressure (bar) Constr. rmsd

3.95109e+00 3.68453e-06

Step Time

199900000 399800.00000

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.66243e+04 8.41650e+04 6.49893e+04 6.19477e+02 -4.30919e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.29324e+04 1.27113e+05 5.95721e+04 -1.50442e+06 5.13644e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13331e+06 2.89694e+05 -8.43614e+05 1.67312e+07 3.02904e+02

Pressure (bar) Constr. rmsd

2.44680e+01 3.68122e-06

Step Time

200000000 400000.00000

Writing checkpoint, step 200000000 at Wed Oct 22 14:37:55 2025

Energies (kJ/mol)

Bond U-B Proper Dih. Improper Dih. CMAP Dih.

1.63211e+04 8.43507e+04 6.50654e+04 6.64856e+02 -5.70809e+01

LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.

1.28909e+04 1.26843e+05 5.70648e+04 -1.50256e+06 5.05957e+03

Potential Kinetic En. Total Energy Conserved En. Temperature

-1.13436e+06 2.89755e+05 -8.44602e+05 1.67400e+07 3.02968e+02

Pressure (bar) Constr. rmsd

-2.41802e+02 3.71154e-06

初始帧：

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991帧：

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992帧

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997帧

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998帧：

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作者
Author: student0618 时间: 2025-10-25 16:48
本帖最后由 student0618 于 2025-10-25 16:53 编辑

先trjconv处理好轨迹pbc，或者vmd 看其他image多肽在哪。

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