Re: [GaMD-discuss] Unexpected large Boost-Energy-Dihedral
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Re: [GaMD-discuss] Unexpected large Boost-Energy-Dihedral
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From: Mehrnoosh K. H. <meh...@jh...> - 2025-06-11 15:12:54
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Dear Dr. Yinglong, Thank you very much for your help. Yes, I am using hydrogen mass repartitioning for preparing my system. Best, Hazrati On Wednesday, June 11, 2025 15:43 CEST, "Miao, Yinglong" <Yin...@me...> wrote: Hi Hazrati, For your input parameters shown in the mdout file: &cntrl imin = 0, !No minimization irest = 1, !Restart the simulation, reading coordinates and velocities fromntx = 5, !Coordinates and velocities will be read from previous files nstlim = 1000500000, !Number of MD-steps to be performed """4000 ns""" dt = 0.004, tol = 0.000001, !The tolerance to use to determine when to stop the minimizatntc = 2, !bonds involving hydrogen are constrained ntf = 2, !to employ TIP3P set NTF = NTC = 2 ig = -1, !The seed for the pseudo-random number generator. the random seed wcut = 10.0, !non-bond cut off ntb = 2, !constant pressure ntp = 1, !isotropic position scaling ntpr = 250000, !Every ntpr steps, energy information will be printed in humantwx = 250000, !Every ntwx steps, the coordinates will be written to the mdcntwr = 250000, !Every ntwr steps during dynamics, the “restrt” file willntwprt = 0, !Include all atoms of the system when writing trajectories ntxo = 1, !Format of the final coordinate. 1 = ASCII, 2 = NetCDF ioutfm = 1, !Format of the coordinate and trajectory files. 1 = Binary NetCDiwrap = 1, !Wrap the molecule into the box. Good for long trajectories ntt = 3, !Thermostat type. 3 = Langevin dynamics gamma_ln = 2.0, !Collision frequency in ps-1 temp0 = 300.0, !Initial Temperature tempi = 300.0, !Aimed T ifsc = 1, !Soft core potential icfe = 1, !The basic flag for free energy calculations gti_cpu_output = 0, gti_add_sc = 1, irest_gamd = 0, igamd = 17, iE = 1, !Set the threshold enrgy to 2=upper bound, 1=lower bound iEP = 1, !Set the threshold enrgy to 2=upper bound, 1=lower bound iED = 1, !Set the threshold enrgy to 2=upper bound, 1=lower bound ntcmdprep = 500000, !2 ns ntcmd = 5000000, !20 ns !ntcmd = 0 ntebprep = 5000000, !20 ns nteb = 1000000000 !4000 ns !nteb = 0 ntave = 250, !every 1 ps sigma0P = 2.0, sigma0D = 6.0, timask1 = ':741-768', !Specifies the atoms unique to V0 in ambmask format. Resscmask1 = ':741-768', !Soft core mask timask2 = '', !Specifies the atoms unique to V1 in ambmask format. scmask2 = '', !Soft core mask bgpro2atm=1, edpro2atm=5647, nmropt = 1, / &wt type='REST', / &wt type='END', / DISANG=dist.RST / I have highlighted those that may cause issues. First, ntave may be too small; it should be roughly 4 times the total number of atoms in your system. Second, you may want to output energies and frames more frequently so that you have ~0.5 - 1 million frames in total from your production simulation for accurate reweighting. Next, for dt=0.004, make sure you have hydrogen mass repartitioning in your prepared system. Otherwise, it’s safer to start with dt=2fs simulations. Finally, you may break such a long simulation into multiple runs, especially separating the equilibration and production. You can find more information about the parameter settings and tutorials at: https://www.med.unc.edu/pharm/miaolab/resources/gamd/manual/, https://www.med.unc.edu/pharm/miaolab/resources/gamd/tutorial/, https://www.med.unc.edu/pharm/miaolab/resources/gamdtutorials/ Hope these help,Yinglong Yinglong Miao, Ph.D. Associate Professor Department of Pharmacology and Computational Medicine Program University of North Carolina - Chapel Hill Tel: 1-919-962-5696 http://miaolab.org Editor-in-Chief npj Drug Discovery https://www.nature.com/npjdrugdiscov ======= For discussion on GaMD, please subscribe to mailing list: https://sourceforge.net/projects/gamd/lists/gamd-discuss, post emails to "gam...@li..." and help others as much as you can! ======= On Jun 10, 2025, at 9:28 AM, Mehrnoosh Khodam Hazrati <meh...@jh...> wrote: Dear Dr. Yinglong, Thank you for your reply. Sorry, the file is large, I'm sending the first lines of the mdout file. Please let me know if I am doing something wrong. Thanks for your time, Best, Hazrati On Tuesday, June 10, 2025 14:08 CEST, "Miao, Yinglong" <Yin...@me...> wrote: HI Hazrati, Could you possibly share a copy of your mdout files, especially for the PPI-GaMD equilibration part? We can look into the issue more … Best,Yinglong Yinglong Miao, Ph.D. Associate Professor Department of Pharmacology and Computational Medicine Program University of North Carolina - Chapel Hill Tel: 1-919-962-5696 http://miaolab.org Editor-in-Chiefnpj Drug Discoveryhttps://www.nature.com/npjdrugdiscov On Jun 9, 2025, at 9:51 AM, Mehrnoosh Khodam Hazrati via GaMD-discuss <gam...@li...> wrote: Dear GaMD developer, Although I am using Amber22 for my simulations with PPI-GaMD-Dual, I get sharp changes in the dihedral energies, no matter if irest=1 or irest=0, and it leads to unexpectedly large Boost-Energy-Dihedral (the 8th column) in my gamd.log files. Since you mentioned in the manual that this bug is already solved in Amber20, I don't expect to face it using Amber22. I get reasonable values for the Boost-Energy-Potential (the 7th column). Do you have any idea if it is the bug or there might be something wrong with my setting? Thanks for your time. Best regards, Hazrati --Mehrnoosh Hazrati, Ph.D. | Czech Academy of SciencesAssociate ScientistE-mail: meh...@jh... _______________________________________________ GaMD-discuss mailing list GaM...@li... https://lists.sourceforge.net/lists/listinfo/gamd-discuss -- --Mehrnoosh Hazrati, Ph.D. | Czech Academy of SciencesAssociate ScientistE-mail: meh...@jh... |
