版块导航: 正在加载中...

登录注册

应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜

返回列表

zyj8119

木虫 (著名写手)

[交流] 【求助】gromacs的一个新问题

版本问题算是解决了，但是又遇到一个新问题：
zyj@zyj-laptop:~/桌面/drg$ grompp -f fullmd.mdp -c minimized_water.gro -p sys.to
p -o fullmd.tpr
                     :-)  G  R  O  M  A  C  S  (-:

            GROningen Mixture of Alchemy and Childrens' Stories

                        :-)  VERSION 4.0.7  (-:

   Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
         Copyright (c) 2001-2008, The GROMACS development team,
         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  (-:

Option    Filename  Type       Description
------------------------------------------------------------
  -f    fullmd.mdp  Input, Opt!  grompp input file with MD parameters
-po    mdout.mdp  Output    grompp input file with MD parameters
  -c minimized_water.gro  Input       Structure file: gro g96 pdb tpr tpb tpa
  -r    conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
-rb    conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n    index.ndx  Input, Opt.  Index file
  -p       sys.top  Input       Topology file
-pp  processed.top  Output, Opt. Topology file
  -o    fullmd.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: 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.
-[no]rmvsbds bool yes    Remove constant bonded interactions with virtual
                        sites
-maxwarn    int 0    Number of allowed warnings during input processing
-[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'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...

NOTE 1 [file fullmd.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

processing topology...
Opening library file /usr/share/gromacs/top/ffG53a6.itp
Opening library file /usr/share/gromacs/top/ffG53a6nb.itp
Opening library file /usr/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations
Opening library file /usr/share/gromacs/top/spce.itp
Opening library file /usr/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'DRG'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 290 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/share/gromacs/top/aminoacids.dat
There are: 46055    OTHER residues
There are:    0 PROTEIN residues
There are:    0       DNA residues
Analysing Other...

-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/readir.c, line: 1069

Fatal error:
137973 atoms are not part of any of the T-Coupling groups
-------------------------------------------------------

"Look at these, my work-strong arms" (P.J. Harvey)

回复此楼

» 猜你喜欢

博士读完未来一定会好吗已经有23人回复
导师想让我从独立一作变成了共一第一已经有7人回复
到新单位后，换了新的研究方向，没有团队，持续积累2区以上论文，能申请到面上吗已经有11人回复
读博已经有4人回复
JMPT 期刊投稿流程已经有4人回复
心脉受损已经有5人回复
Springer期刊投稿求助已经有4人回复
小论文投稿已经有3人回复
申请2026年博士已经有6人回复

» 本主题相关价值贴推荐，对您同样有帮助:

Gromacs中，mdrun出错已经有5人回复
在gromacs中运行mdrun命令时出错已经有10人回复
分子模拟时间越长越好吗？已经有44人回复
【求助】gromacs周期性边界条件问题已经有9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
【求助】gromacs的又一个问题已经有22人回复
【求助】gromacs出现了一个问题已经有10人回复
【求助】求助Gromacs中关于g_hbond的out文件的问题已经有10人回复
【求助】有关gromacs得两个问题已经有10人回复
【求助】理论与计算化学新手求教已经有13人回复

» 抢金币啦！回帖就可以得到:
查看全部散金贴

1楼2011-01-07 18:00:51

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

zyj8119

木虫 (著名写手)

引用回帖:

Originally posted by zyj8119 at 2011-01-07 18:00:51:
版本问题算是解决了，但是又遇到一个新问题：
zyj@zyj-laptop:~/桌面/drg$ grompp -f fullmd.mdp -c minimized_water.gro -p sys.to
p -o fullmd.tpr
:-) G R O M A C S (-: ...

zyj@zyj-laptop:~/桌面/drg$ ls
drg.gro    md.log       minimized_box.gro minim_traj.trr  #sys.top.1#
drg.itp    mdout.mdp    minimized.gro       out.gro
fullmd.mdp  #mdout.mdp.1# minimized_water.gro  sys.top
input.tpr minim_ener.edr  minim.mdp          sys.top~

赞一下

回复此楼

2楼2011-01-07 18:02:24

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

zyj8119

木虫 (著名写手)

引用回帖:

Originally posted by zyj8119 at 2011-01-07 18:02:24:

zyj@zyj-laptop:~/桌面/drg$ ls
drg.gro    md.log       minimized_box.gro minim_traj.trr  #sys.top.1#
drg.itp    mdout.mdp    minimized.gro       out.gro
fullmd.mdp  #mdout.mdp.1# ...

此问题也解决了，是temperature coupling的问题。

赞一下

回复此楼

3楼2011-01-07 23:17:58

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

相关版块跳转我要订阅楼主 zyj8119 的主题更新

返回列表

24小时热门版块排行榜

zyj8119

[交流] 【求助】gromacs的一个新问题

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:

» 抢金币啦！回帖就可以得到:查看全部散金贴

zyj8119

zyj8119

» 抢金币啦！回帖就可以得到:
查看全部散金贴