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604758762鐵桿木蟲(chóng) (正式寫(xiě)手)
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[求助]
Gromacs水中的溶菌酶npt平衡出錯(cuò)
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RT，nvt平衡可以正常運(yùn)行，但是到npt平衡時(shí)，會(huì)出錯(cuò)，grompp終止運(yùn)行 下面是命令及錯(cuò)誤信息： [wanghj@c0103 donglixue]$ grompp_mpi -f npt.mdp -c em.gro -t nvt.cpt -p topol.top -o npt.tpr :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, P盲r Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description ------------------------------------------------------------ -f npt.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c em.gro Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o npt.tpr Output Run input file: tpr tpb tpa -t nvt.cpt Input, Opt! Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Analysing residue names: There are: 129 Protein residues There are: 10824 Water residues There are: 8 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group Protein is 3895.83 Number of degrees of freedom in T-Coupling group non-Protein is 64965.17 WARNING 1 [file npt.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 6.300 Using frame at t = 6.3 ps Starting time for run is 0 ps Largest charge group radii for Van der Waals: 0.163, 0.160 nm Largest charge group radii for Coulomb: 0.172, 0.165 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 45x45x45, spacing 0.156 0.156 0.156 Estimate for the relative computational load of the PME mesh part: 0.25 This run will generate roughly 399 Mb of data There was 1 warning ------------------------------------------------------- Program grompp_mpi, VERSION 4.5.5 Source code file: grompp.c, line: 1584 Fatal error: Too many warnings (1), grompp_mpi terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "I Caught It In the Face" (P.J. Harvey) 但是在在命令后面加-maxwarn 3 時(shí)，即 grompp_mpi -f npt.mdp -c em.gro -t nvt.cpt -p topol.top -o npt.tpr -maxwarn 3就可以正常了，請(qǐng)問(wèn)這個(gè)錯(cuò)誤該怎么解決呢？ |
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2樓2012-04-26 10:00:34
604758762
鐵桿木蟲(chóng) (正式寫(xiě)手)
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3樓2012-04-26 10:54:29
andylau286
鐵蟲(chóng) (小有名氣)
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【答案】應(yīng)助回帖
★ ★ ★ ★ ★
感謝參與，應(yīng)助指數(shù) +1
zh1987hs: 金幣+2, 謝謝 2012-04-26 21:15:03
604758762: 金幣+3, ★有幫助 2012-05-03 21:11:50
感謝參與，應(yīng)助指數(shù) +1
zh1987hs: 金幣+2, 謝謝 2012-04-26 21:15:03
604758762: 金幣+3, ★有幫助 2012-05-03 21:11:50
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WARNING 1 [file npt.mdp]: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option 這個(gè)不算錯(cuò)誤，只是系統(tǒng)提示你，你正在用壓力耦合，這會(huì)給系統(tǒng)帶來(lái)人工成分，可能會(huì)影響到嚴(yán)謹(jǐn)性。 但這個(gè)錯(cuò)誤是無(wú)害的，可以在命令的最后加 “ -maxwarn 1 "就可以運(yùn)行了， |
4樓2012-04-26 21:11:19
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