 |
 |
 |
 |
 |
 |
||
 |
 |
 |
 |
 |
| 6 | 1/1 | 返回列表 |
| 查看: 1340 | 回復(fù): 5 | |||
s6120610021銅蟲 (小有名氣)
|
[求助]
水中溶菌酶教程遇見錯誤，求指教
|
|
大家好 我是新手 在水中溶菌酶的教程中在第六步平衡中 輸入grompp_mpi -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -c 后面輸入em.gro代表什么意思？ em.gro 能量最小化結(jié)構(gòu) grompp_mpi -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) 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 nvt.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 nvt.tpr Output Run input file: tpr tpb tpa -t traj.trr 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.12# 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... Setting gen_seed to 19890 Velocities were taken from a Maxwell distribution at 300 K 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 Largest charge group radii for Van der Waals: 0.165, 0.156 nm Largest charge group radii for Coulomb: 0.165, 0.164 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 Back Off! I just backed up nvt.tpr to ./#nvt.tpr.5# gcq#133: "You Fill Your Space So Sweet" (F. Apple) 求指教錯誤原因 |
回復(fù)此樓» 收錄本帖的淘帖專輯推薦
 Gromacs |
» 猜你喜歡
0856求調(diào)劑
已經(jīng)有13人回復(fù)
-
0703化學(xué)
已經(jīng)有11人回復(fù)
-
329求調(diào)劑
已經(jīng)有7人回復(fù)
-
321求調(diào)劑
已經(jīng)有8人回復(fù)
-
0856材料化工調(diào)劑 總分330
已經(jīng)有12人回復(fù)
-
309求調(diào)劑
已經(jīng)有3人回復(fù)
-
070300化學(xué)354求調(diào)劑
已經(jīng)有4人回復(fù)
-
330分求調(diào)劑
已經(jīng)有3人回復(fù)
-
299求調(diào)劑
已經(jīng)有8人回復(fù)
-
一志愿北京理工大學(xué)本科211材料工程294求調(diào)劑
已經(jīng)有6人回復(fù)
» 本主題相關(guān)價值貼推薦，對您同樣有幫助:
- 高斯 NtrErr Called from FileIO.錯誤。優(yōu)化可完成頻率計算失敗，求指教!!
已經(jīng)有7人回復(fù)
- 出現(xiàn)301錯誤，求指教
已經(jīng)有8人回復(fù)
- 計算結(jié)果死在了l101這個地方，但是我的命令行沒有錯誤呀，求指教！
已經(jīng)有13人回復(fù)
- 【求助】求高人指教 這個錯誤怎么改
已經(jīng)有11人回復(fù)
2樓2013-01-17 22:08:12
s6120610021
銅蟲 (小有名氣)
- 應(yīng)助: 5 (幼兒園)
- 金幣: 1.2
- 散金: 60
- 帖子: 257
- 在線: 122小時
- 蟲號: 2020477
- 注冊: 2012-09-22
- 專業(yè): 能源化工
3樓2013-01-18 09:47:09
4樓2013-01-18 11:25:08
yaozhq
金蟲 (小有名氣)
- 應(yīng)助: 126 (高中生)
- 金幣: 1137.8
- 紅花: 7
- 帖子: 260
- 在線: 37.6小時
- 蟲號: 1475454
- 注冊: 2011-11-04
- 性別: GG
- 專業(yè): 生物大分子結(jié)構(gòu)與功能
5樓2013-01-18 14:29:44
s6120610021
銅蟲 (小有名氣)
- 應(yīng)助: 5 (幼兒園)
- 金幣: 1.2
- 散金: 60
- 帖子: 257
- 在線: 122小時
- 蟲號: 2020477
- 注冊: 2012-09-22
- 專業(yè): 能源化工
6樓2013-01-20 16:56:19
相關(guān)版塊跳轉(zhuǎn)
我要訂閱樓主 s6120610021 的主題更新
| 6 | 1/1 | 返回列表 |
| 最具人氣熱帖推薦 [查看全部] | 作者 | 回/看 | 最后發(fā)表 | |
|---|---|---|---|---|
|
[碩博家園] 招收生物學(xué)/細(xì)胞生物學(xué)調(diào)劑 +4 | IceGuo 2026-03-26 | 5/250 |
|
|---|---|---|---|---|
|
[考研] 332求調(diào)劑 +6 | 蕉蕉123 2026-03-28 | 6/300 |
|
|
|
[考研] 085602 化工專碩 338分 求調(diào)劑 +12 | 路癡小琪 2026-03-27 | 12/600 |
|
|
|
[考研] 材料與化工272求調(diào)劑 +9 | 阿斯蒂芬2004 2026-03-28 | 9/450 |
|
|
|
[考研] 394求調(diào)劑 +3 | 好事多磨靜候佳?/a> 2026-03-26 | 5/250 |
|
|
|
[考研] 0856，材料與化工321分求調(diào)劑 +12 | 大饞小子 2026-03-27 | 13/650 |
|
|
|
[考研]
 材料與化工考研調(diào)劑
+17
|
孅華 2026-03-22 | 17/850 |
|
|
|
[考研] 085701環(huán)境工程求調(diào)劑 +9 | 多久上課 2026-03-27 | 9/450 |
|
|
|
[考研] 330一志愿中國海洋大學(xué) 化學(xué)工程 085602 有讀博意愿 求調(diào)劑 +3 | wywy.. 2026-03-27 | 4/200 |
|
|
|
[考研]
材料學(xué)碩，求調(diào)劑
 6+5
|
糖葫蘆888ll 2026-03-22 | 10/500 |
|
|
|
[考研]
304材料求調(diào)劑
+4
|
鐘llll 2026-03-26 | 4/200 |
|
|
|
[考研] 309求調(diào)劑 +4 | gajsj 2026-03-25 | 5/250 |
|
|
|
[考研] 07化學(xué)303求調(diào)劑 +5 | 睿08 2026-03-25 | 5/250 |
|
|
|
[考研] 332求調(diào)劑 +6 | 032500 2026-03-25 | 6/300 |
|
|
|
[考研] 考研一志愿蘇州大學(xué)初始315（英一）求調(diào)劑 +3 | sbdksD 2026-03-24 | 4/200 |
|
|
|
[考研] 求調(diào)劑 +3 | 李李不服輸 2026-03-25 | 3/150 |
|
|
|
[考研] 生物學(xué)學(xué)碩求調(diào)劑 +7 | 小羊睡著了? 2026-03-23 | 10/500 |
|
|
|
[考研] 調(diào)劑 +4 | 13853210211 2026-03-24 | 4/200 |
|
|
|
[考研] 292求調(diào)劑 +4 | 鵝鵝鵝額額額額?/a> 2026-03-24 | 4/200 |
|
|
|
[考博] 26申博自薦 +3 | whh869393 2026-03-24 | 3/150 |
|