Dear Amber Developers and Users,
I fixed this problem by myself. The problem is caused by dt setting. In my heating input file, I set dt=0.002 but it work well at dt=0.001. I am not sure what reason. Could it be that the step interval is too large and the system is discontinuous? Please let me know if anyone knows!
Thanks,
Jiafan Guo
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发件人: 郭 家藩 via AMBER <amber.ambermd.org>
发送时间: 2024年3月16日 19:47
收件人: amber.ambermd.org <amber.ambermd.org>
主题: [AMBER] NaN error during heating in building 12-6-4 LJ multisite Mg2+ model of DNA gyrase.
Dear Amber Developers and Users,
I am trying to build a 12-6-4 LJ multisite Mg2+ model of DNA gyrase. I get the parameters of Mg2+ dummy atom model from articles:
Zuo Z, Liu J. Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease. J Chem Inf Model. 2019 Jan 28;59(1):399-408. doi: 10.1021/acs.jcim.8b00627. Epub 2018 Dec 19. PMID: 30521334.
Liao Q, Pabis A, Strodel B, Kamerlin SCL. Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions. J Phys Chem Lett. 2017 Nov 2;8(21):5408-5414. doi: 10.1021/acs.jpclett.7b02358. Epub 2017 Oct 23. PMID: 29022713; PMCID: PMC5672556.
At the same time I referred the tutorial of Zinc cationic dummy atom method. I generated the prmtop and inpcrd by tleap successfully. The system was also successfully minimized by pmemd.cuda. But heating is failed.
In order to find out what could be causing the problem, I build a solution system only contain the Mg and its dummy atoms. When the system is heated to about 150 ℃, the TEMP of system will change drastically and then NaN. In the trajectory, I saw the bonds between dummy atom around Mg atom are distorted.
------------------------------------------------------------------------------
NSTEP = 42600 TIME(PS) = 85.200 TEMP(K) = 158.24 PRESS = 0.0
Etot = -797598.2830 EKtot = 69122.8203 EPtot = -866721.1033
BOND = 8264.9383 ANGLE = 9870.1316 DIHED = 8546.4412
UB = 0.0000 IMP = 0.0000 CMAP = 1380.0426
1-4 NB = 5304.4898 1-4 EEL = 40187.1610 VDWAALS = 157817.8662
EELEC = -1098092.1739 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NSTEP = 42700 TIME(PS) = 85.400 TEMP(K) = 4686.87 PRESS = 0.0
Etot = ************** EKtot = 2047368.2500 EPtot = **************
BOND = 2174141.0358 ANGLE = 61063.3395 DIHED = 10953.6808
UB = 0.0000 IMP = 0.0000 CMAP = 1467.8011
1-4 NB = ************** 1-4 EEL = 40284.5824 VDWAALS = **************
EELEC = -1097351.5454 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
NSTEP = 42800 TIME(PS) = 85.600 TEMP(K) = NaN PRESS = 0.0
Etot = NaN EKtot = NaN EPtot = **************
BOND = ************** ANGLE = 2940719.7361 DIHED = 67434.7685
UB = 0.0000 IMP = 0.0000 CMAP = 2725.7645
1-4 NB = 494048912.1324 1-4 EEL = 17575.0600 VDWAALS = **************
EELEC = -69105.1738 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
I've tried everything I could possibly think of that and nothing has solved this problem. I would like someone to point out where there is a problem with my operation. All relevant documents are attached.
Best regards,
Jiafan Guo
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Received on Sat Mar 16 2024 - 22:00:02 PDT
