| 查看: 4623 | 回复: 22 | |||
| 当前只显示满足指定条件的回帖，点击这里查看本话题的所有回帖 | |||
[交流]
【求助】gromacs的又一个问题
|
|||
|
我运行 gromcs,现在是没有原子数不等的问题了，但是又出现了这个问题： 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 (-: Option Filename Type Description ------------------------------------------------------------ -f minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c total.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p sys.top Input Topology file -pp processed.top Output, Opt. Topology file -o input.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... ' for variable optimize_fft, using 'no' Next time use one of: 'no' 'yes' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for drg 64 turning H bonds into constraints... Excluding 2 bonded neighbours for SOL 218 turning H bonds into constraints... processing coordinates... double-checking input for internal consistency... WARNING 1 [file "sys.top", line 37]: For minimization with LINCS constraints, lincs_iter should be 4 to 8. There was 1 warning ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 1109 Fatal error: There were 1 error(s) processing your input ------------------------------------------------------- "Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw) 我的sys.top是： ; ; File 'sys.top' was generated ; By user: zhu (503) ; On host: apollo2 ; At date: Wed Mar 12 15:48:05 2008 ; ; This is your topology file ; DRG ; ; Include forcefield parameters #include "ffG53a6.itp" ; Include surfacetant topology #include "drg.itp" ; Include water topology #include "spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name aok in water [ molecules ] ; Compound #mols drg 64 SOL 218 ，而minim.mdp文件为： ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization of AOK ; Title of run ; The following lines tell the program the standard locations where to find cert ain files cpp = /lib/cpp ; Preprocessor include = -I../top ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimizati on) emtol = 1000.0 ; Stop minimization when the maximum force < 3000.0 kJ /mol nsteps = 100000 ; Maximum number of (minimization) steps to perf orm nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout step s xtc_grps = system ; Which coordinate group(s) to write to d isk energygrps = system ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calcul ate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, gri d) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interact ions rcoulomb = 1.0 fourierspacing =0.12 pme_order =4 ewald_rtol =1e-5 optimize_fft =yes rvdw = 1.0 ; long range Van der Waals cut-off constraints = hbonds ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) ;freeze ;freezegrps = SOL |
回复此楼» 猜你喜欢
售SCI一区文章，我:8.O.551.O.5.4,科目全,可伽急
已经有7人回复
-
售一区SCI文章T0P，我:8O.551.O54,科目全,可十急
已经有8人回复
-
售SCI一区T0P文章，我:8O.55.1.O.54,科目全,可伽急
已经有11人回复
-
售SCI一区文章，我:8.O.551.O.5.4,科目全,可伽急
已经有6人回复
-
售SCI文章，我:8O.5.5.1O.54,科目全,可十急
已经有8人回复
-
售SCI文章，我:8O.5.5.1O.54,科目全,可十急
已经有5人回复
-
售SCI一区T0P文章，我:8O.55.1.O.5.4,科目齐全,可+急
已经有10人回复
-
售SCI一区T0P文章，我:8.O55.1.O.54,科目全,可十急
已经有8人回复
-
国社科又开始会评了，不知道这次命运如何
已经有14人回复
-
售SCI一区文章，我:8.O.55.1.O.54,科目齐全,可伽急
已经有8人回复
» 本主题相关价值贴推荐，对您同样有帮助:
- Gromacs中加入离子
已经有5人回复
- [新手求教]安装Gromacs后，查看pdb2gmx命令，显示无此命令
已经有9人回复
- 【讨论】gromacs电荷不为整数
已经有6人回复
- 【求助】这是我安装gromacs过程，但是出错阿，这个怎么办呢？谢谢
已经有11人回复
- 【原创】在gromacs的gro中插入小分子
已经有12人回复
- 【求助】gromacs出现了一个问题
已经有10人回复
- 【求助】求一个gromacs的中文教程，包括安装的部分，小弟新手，从零学起
已经有8人回复
- 【求助】Gromacs和NAMD比Amber快很多吗？如何选择？
已经有7人回复
» 抢金币啦！回帖就可以得到:
-
南京大学医学院附属鼓楼医院 肿瘤疫苗与纳米医学团队 博士后招聘
+1/92
-
上海交通大学周宝文课题组招收2027年申请考核制博士研究生
+1/89
-
课题组招推免硕士和直博生。华中科技大学光电学院发光材料与器件团队。
+1/89
-
武汉大学高等研究院超分子化学与材料课题组2027级招收硕士和博士研究生及研究助理
+1/84
-
湖南大学电镜中心招收2027年推免直博生
+1/70
-
重庆大学招岩土工程科研博士后，基本薪酬一年40万+，另据论文与项目发放奖励
+1/30
-
神经生物学，基础医学，科研助理招聘
+1/21
-
评职称需要，卖发明专利了:D有技术储备需求的设备厂商可联系
+1/18
-
新加坡国立大学Sibudjing Kawi教授课题组招聘博士后（热催化/等离子体催化方向）
+1/11
-
新加坡国立大学Sibudjing Kawi教授课题组part-time PhD（热催化/等离子体催化方向）
+1/8
-
石蜡切片VS冰冻切片：哪种更适合免疫荧光检测？
+1/7
-
北京科技大学能源与环境工程学院 博士、博士后招聘启事
+1/7
-
深圳大学岩土多场耦合课题组-长期招聘研究生、博士后、专职研究人员
+1/6
-
浙江大学招聘2027年生物医学工程直博生
+1/5
-
香港大学先进制造实验室招收（机械类/机电一体化等专业）27年度博士和硕士研究生
+1/5
-
上海交通大学纳米光子学实验室招收直博生（2027级）
+1/4
-
【科研诚信】武汉轻工大学何江玲3篇论文：涉嫌抄袭、成组数据重复、制造虚假显著
+1/3
-
慢性阻塞性肺疾病（COPD）多因子蛋白检测：挖掘炎症损伤分子机制
+1/2
-
半导体器件模拟与EDA工具开发及AI大模型本地部署：从器件物理到算力工作站配置方案
+1/2
-
结肠炎多维度分子解析：炎症‑免疫‑肠道屏障一体化检测策略
+1/1
17楼2011-01-06 10:36:12
2楼2010-12-22 15:18:04
3楼2010-12-22 16:10:49
4楼2010-12-22 16:54:22
简单回复
matao01114楼
2011-01-01 01:09
回复
zyj8119(金币+1):谢谢参与
