Dear Alex Can you please tell me how to pack a bilayer lipid molecule around the protein. Because bad contact is coming due to the code for shrinking the box. During minimization the lipid bilayer should move from protein c-alpha atoms. If you have any paper related to that please send me the link
On Wed 22 Aug, 2018, 11:26 AM Alex, <nedoma...@gmail.com> wrote: > Before you go on to listen to bad advice and recompile Gromacs in double > precision, the errors you're getting during minimization are _much_ more > likely to come from a bad initial state of your system. > > Alex > > > On 8/21/2018 11:51 PM, Bratin Kumar Das wrote: > > Dear Rahul, > > Thinking you for your suggestion. I don't know how to > > use double precision. can you please share some link for that > > > > On Wed, Aug 22, 2018 at 11:02 AM, RAHUL SURESH <drrahulsur...@gmail.com> > > wrote: > > > >> Hi. > >> > >> As gromacs suggested try double precision. > >> > >> Thank you > >> > >> On Wed, 22 Aug 2018 at 10:36 AM, Bratin Kumar Das < > >> 177cy500.bra...@nitk.edu.in> wrote: > >> > >>> Dear All, > >>> I am simulating a membrane protein which have > extracellular > >>> domain, TMD(trans membrane domain) and a extracellular domain. After > >>> packing the POPC molecules around the protein, I solvated the system. > I > >>> removed all the waters from the POPC portion and added ions to > neutralise > >>> the system. During the energy minimisation the following errors are > >> coming > >>> > >>> GROMACS is written by: > >>> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par > >>> Bjelkmar > >>> Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit > >> Groenhof > >>> Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios > >>> Karkoulis > >>> Peter Kasson Jiri Kraus Carsten Kutzner Per > Larsson > >>> Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik > Marklund > >>> Teemu Murtola Szilard Pall Sander Pronk Roland > Schulz > >>> Alexey Shvetsov Michael Shirts Alfons Sijbers Peter > >> Tieleman > >>> Teemu Virolainen Christian Wennberg Maarten Wolf > >>> and the project leaders: > >>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > >>> > >>> Copyright (c) 1991-2000, University of Groningen, The Netherlands. > >>> Copyright (c) 2001-2017, The GROMACS development team at > >>> Uppsala University, Stockholm University and > >>> the Royal Institute of Technology, Sweden. > >>> check out http://www.gromacs.org for more information. > >>> > >>> GROMACS is free software; you can redistribute it and/or modify it > >>> under the terms of the GNU Lesser General Public License > >>> as published by the Free Software Foundation; either version 2.1 > >>> of the License, or (at your option) any later version. > >>> > >>> GROMACS: gmx mdrun, version 2016.5 > >>> Executable: /usr/local/gromacs/bin/gmx > >>> Data prefix: /usr/local/gromacs > >>> Working dir: > >>> /home/workstation/Documents/GROMACS_projects/g_protein_ > >> class_b_sim_gromacs > >>> Command line: > >>> gmx mdrun -v -s energy_minim.tpr -deffnm energy_minim > >>> > >>> > >>> Running on 1 node with total 4 cores, 4 logical cores > >>> Hardware detected: > >>> CPU info: > >>> Vendor: Intel > >>> Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz > >>> SIMD instructions most likely to fit this hardware: AVX2_256 > >>> SIMD instructions selected at GROMACS compile time: AVX2_256 > >>> > >>> Hardware topology: Basic > >>> > >>> Reading file energy_minim.tpr, VERSION 2016.5 (single precision) > >>> Using 1 MPI thread > >>> Using 4 OpenMP threads > >>> > >>> > >>> Steepest Descents: > >>> Tolerance (Fmax) = 1.00000e+02 > >>> Number of steps = 50000 > >>> > >>> WARNING: Listed nonbonded interaction between particles 6334 and 6358 > >>> at distance 4.241 which is larger than the table limit 2.200 nm. > >>> > >>> This is likely either a 1,4 interaction, or a listed interaction inside > >>> a smaller molecule you are decoupling during a free energy calculation. > >>> Since interactions at distances beyond the table cannot be computed, > >>> they are skipped until they are inside the table limit again. You will > >>> only see this message once, even if it occurs for several interactions. > >>> > >>> IMPORTANT: This should not happen in a stable simulation, so there is > >>> probably something wrong with your system. Only change the > >> table-extension > >>> distance in the mdp file if you are really sure that is the reason. > >>> > >>> > >>> Step= 0, Dmax= 1.0e-02 nm, Epot= 7.97855e+11 Fmax= 2.74610e+14, > atom= > >>> 3647 > >>> Step= 1, Dmax= 1.0e-02 nm, Epot= 4.26666e+09 Fmax= 7.52956e+11, > atom= > >>> 3647 > >>> Step= 2, Dmax= 1.2e-02 nm, Epot= 1.33982e+08 Fmax= 1.49946e+10, > atom= > >>> 2036 > >>> Step= 3, Dmax= 1.4e-02 nm, Epot= 2.28974e+07 Fmax= 9.37337e+08, > atom= > >>> 3647 > >>> Step= 4, Dmax= 1.7e-02 nm, Epot= 4.48769e+06 Fmax= 3.34151e+07, > atom= > >>> 13662 > >>> Step= 5, Dmax= 2.1e-02 nm, Epot= 3.37628e+06 Fmax= 3.28448e+06, > atom= > >>> 3645 > >>> Step= 6, Dmax= 2.5e-02 nm, Epot= 3.10830e+06 Fmax= 1.71706e+06, > atom= > >>> 6356 > >>> Step= 7, Dmax= 3.0e-02 nm, Epot= 2.96689e+06 Fmax= 1.68266e+06, > atom= > >>> 6356 > >>> Step= 8, Dmax= 3.6e-02 nm, Epot= 2.83736e+06 Fmax= 1.63442e+06, > atom= > >>> 6356 > >>> Step= 9, Dmax= 4.3e-02 nm, Epot= 2.70582e+06 Fmax= 1.59406e+06, > atom= > >>> 6356 > >>> Step= 10, Dmax= 5.2e-02 nm, Epot= 2.57016e+06 Fmax= 6.10145e+06, > atom= > >>> 68387 > >>> > >>> step 11: One or more water molecules can not be settled. > >>> Check for bad contacts and/or reduce the timestep if appropriate. > >>> > >>> Back Off! I just backed up step11b.pdb to ./#step11b.pdb.3# > >>> > >>> Back Off! I just backed up step11c.pdb to ./#step11c.pdb.3# > >>> Wrote pdb files with previous and current coordinates > >>> Step= 12, Dmax= 3.1e-02 nm, Epot= 2.52760e+06 Fmax= 1.57824e+06, > atom= > >>> 6356 > >>> Step= 13, Dmax= 3.7e-02 nm, Epot= 2.41877e+06 Fmax= 3.20637e+06, > atom= > >>> 68387 > >>> Step= 14, Dmax= 4.5e-02 nm, Epot= 2.39232e+06 Fmax= 1.51717e+06, > atom= > >>> 6356 > >>> Step= 15, Dmax= 5.3e-02 nm, Epot= 2.25380e+06 Fmax= 5.76014e+06, > atom= > >>> 6358 > >>> Step= 16, Dmax= 6.4e-02 nm, Epot= 2.23708e+06 Fmax= 1.48175e+06, > atom= > >>> 6358 > >>> Step= 17, Dmax= 7.7e-02 nm, Epot= 2.00861e+06 Fmax= 1.06806e+06, > atom= > >>> 6358 > >>> Step= 18, Dmax= 9.2e-02 nm, Epot= 1.89692e+06 Fmax= 3.69159e+06, > atom= > >>> 6358 > >>> Step= 19, Dmax= 1.1e-01 nm, Epot= 1.75521e+06 Fmax= 1.19996e+06, > atom= > >>> 6358 > >>> Step= 20, Dmax= 1.3e-01 nm, Epot= 1.47811e+06 Fmax= 3.67398e+06, > atom= > >>> 8027 > >>> Step= 22, Dmax= 8.0e-02 nm, Epot= 1.45234e+06 Fmax= 2.18802e+06, > atom= > >>> 6356 > >>> Step= 23, Dmax= 9.6e-02 nm, Epot= 1.42778e+06 Fmax= 1.22861e+07, > atom= > >>> 6285 > >>> Step= 24, Dmax= 1.2e-01 nm, Epot= 1.39384e+06 Fmax= 1.16780e+06, > atom= > >>> 6358 > >>> Step= 26, Dmax= 6.9e-02 nm, Epot= 1.22389e+06 Fmax= 1.01826e+06, > atom= > >>> 6356 > >>> Step= 27, Dmax= 8.3e-02 nm, Epot= 1.05663e+06 Fmax= 8.23676e+05, > atom= > >>> 6358 > >>> Step= 28, Dmax= 9.9e-02 nm, Epot= 9.00862e+05 Fmax= 4.41513e+06, > atom= > >>> 6285 > >>> Step= 30, Dmax= 6.0e-02 nm, Epot= 8.78491e+05 Fmax= 9.03216e+05, > atom= > >>> 6356 > >>> Step= 31, Dmax= 7.2e-02 nm, Epot= 7.32139e+05 Fmax= 8.20015e+05, > atom= > >>> 6285 > >>> Step= 32, Dmax= 8.6e-02 nm, Epot= 6.90801e+05 Fmax= 7.16405e+06, > atom= > >>> 6285 > >>> Step= 33, Dmax= 1.0e-01 nm, Epot= 6.01138e+05 Fmax= 7.02733e+05, > atom= > >>> 6358 > >>> Step= 34, Dmax= 1.2e-01 nm, Epot= 4.08422e+05 Fmax= 6.19177e+05, > atom= > >>> 6356 > >>> Step= 35, Dmax= 1.5e-01 nm, Epot= 2.39180e+05 Fmax= 8.93953e+06, > atom= > >>> 6356 > >>> Step= 36, Dmax= 1.8e-01 nm, Epot= 1.77754e+05 Fmax= 4.65642e+05, > atom= > >>> 6356 > >>> Step= 37, Dmax= 2.1e-01 nm, Epot= 9.49342e+03 Fmax= 7.65517e+06, > atom= > >>> 6356 > >>> Step= 39, Dmax= 1.3e-01 nm, Epot= -1.01297e+05 Fmax= 3.21496e+05, > atom= > >>> 6357 > >>> > >>> step 40: One or more water molecules can not be settled. > >>> Check for bad contacts and/or reduce the timestep if appropriate. > >>> > >>> Back Off! I just backed up step40b.pdb to ./#step40b.pdb.2# > >>> > >>> Back Off! I just backed up step40c.pdb to ./#step40c.pdb.2# > >>> Wrote pdb files with previous and current coordinates > >>> Step= 41, Dmax= 7.7e-02 nm, Epot= -1.70370e+05 Fmax= 1.79323e+06, > atom= > >>> 6532 > >>> Step= 43, Dmax= 4.6e-02 nm, Epot= -1.94365e+05 Fmax= 2.98882e+05, > atom= > >>> 6357 > >>> Step= 44, Dmax= 5.5e-02 nm, Epot= -2.50520e+05 Fmax= 1.07420e+06, > atom= > >>> 6551 > >>> Step= 45, Dmax= 6.6e-02 nm, Epot= -2.65915e+05 Fmax= 2.73365e+05, > atom= > >>> 6357 > >>> Step= 46, Dmax= 8.0e-02 nm, Epot= -3.58321e+05 Fmax= 2.46276e+05, > atom= > >>> 6357 > >>> Step= 47, Dmax= 9.6e-02 nm, Epot= -4.33618e+05 Fmax= 6.66792e+05, > atom= > >>> 6285 > >>> Step= 48, Dmax= 1.1e-01 nm, Epot= -4.45739e+05 Fmax= 6.65627e+05, > atom= > >>> 6285 > >>> > >>> step 49: One or more water molecules can not be settled. > >>> Check for bad contacts and/or reduce the timestep if appropriate. > >>> > >>> Back Off! I just backed up step49b.pdb to ./#step49b.pdb.2# > >>> > >>> Back Off! I just backed up step49c.pdb to ./#step49c.pdb.2# > >>> Wrote pdb files with previous and current coordinates > >>> Step= 50, Dmax= 6.9e-02 nm, Epot= -4.86014e+05 Fmax= 3.28474e+05, > atom= > >>> 6285 > >>> Step= 51, Dmax= 8.3e-02 nm, Epot= -5.04696e+05 Fmax= 2.93639e+06, > atom= > >>> 6272 > >>> Step= 52, Dmax= 9.9e-02 nm, Epot= -5.45904e+05 Fmax= 1.87021e+05, > atom= > >>> 6357 > >>> Step= 53, Dmax= 1.2e-01 nm, Epot= -6.52906e+05 Fmax= 2.72180e+05, > atom= > >>> 6357 > >>> Step= 55, Dmax= 7.1e-02 nm, Epot= -7.07692e+05 Fmax= 1.08267e+07, > atom= > >>> 3569 > >>> Step= 62, Dmax= 1.3e-03 nm, Epot= -7.60656e+05 Fmax= 1.19350e+08, > atom= > >>> 11335 > >>> Step= 65, Dmax= 4.0e-04 nm, Epot= -7.60669e+05 Fmax= 3.94493e+07, > atom= > >>> 3569 > >>> Step= 69, Dmax= 6.0e-05 nm, Epot= -7.60669e+05 Fmax= 1.55572e+07, > atom= > >>> 35695 > >>> Step= 70, Dmax= 7.2e-05 nm, Epot= -7.60670e+05 Fmax= 1.30303e+07, > atom= > >>> 11335 > >>> Step= 71, Dmax= 8.7e-05 nm, Epot= -7.60677e+05 Fmax= 2.11985e+07, > atom= > >>> 3569 > >>> Step= 72, Dmax= 1.0e-04 nm, Epot= -7.60678e+05 Fmax= 1.99492e+07, > atom= > >>> 11335 > >>> Step= 73, Dmax= 1.2e-04 nm, Epot= -7.60686e+05 Fmax= 2.93949e+07, > atom= > >>> 3569 > >>> Step= 74, Dmax= 1.5e-04 nm, Epot= -7.60686e+05 Fmax= 2.98387e+07, > atom= > >>> 11335 > >>> Step= 75, Dmax= 1.8e-04 nm, Epot= -7.60696e+05 Fmax= 4.12585e+07, > atom= > >>> 3569 > >>> Step= 83, Dmax= 1.7e-06 nm, Epot= -7.60696e+05 Fmax= 4.05617e+07, > atom= > >>> 35695 > >>> Energy minimization has stopped, but the forces have not converged to > the > >>> requested precision Fmax < 100 (which may not be possible for your > >> system). > >>> It stopped because the algorithm tried to make a new step whose size > was > >>> too > >>> small, or there was no change in the energy since last step. Either > way, > >> we > >>> regard the minimization as converged to within the available machine > >>> precision, given your starting configuration and EM parameters. > >>> > >>> Double precision normally gives you higher accuracy, but this is often > >> not > >>> needed for preparing to run molecular dynamics. > >>> You might need to increase your constraint accuracy, or turn > >>> off constraints altogether (set constraints = none in mdp file) > >>> > >>> writing lowest energy coordinates. > >>> > >>> Steepest Descents converged to machine precision in 84 steps, > >>> but did not reach the requested Fmax < 100. > >>> Potential Energy = -7.6069581e+05 > >>> Maximum force = 4.1258524e+07 on atom 3569 > >>> Norm of force = 1.6956947e+05 > >>> > >>> GROMACS reminds you: "If you want to destroy my sweater, hold this > thread > >>> as I walk away." (Weezer) > >>> > >>> I can't understand what is the problem inside the system. Because of > this > >>> reason I can't proceed to equilibration step. please help me. > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >> -- > >> *Regards,* > >> *Rahul * > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at http://www.gromacs.org/ > >> Support/Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? 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