jerkwin/gmxtools

tools for GROMACS

gmxtools

scripts/programs/utilities/tools for GROMACS

Introduction

Tools

Introduction

This is a collection of the tools I used for GROMACS. Hope it helps for you as well.

If you use one/some of the tools for your publication(s), I will appreciate if you cite the Zenodo DOI 10.5281/zenodo.6408973

Tools

名称 NAME	说明 INSTRUCTION	代码 CODE	示例 EXAMPLE
calc	在线计算兼单位换算器	calc gnuECharts
wvmd	自动调整VMD窗口的位置和大小	wvmd.zip
graphene	石墨烯：建模, 几何性质及力场模拟 石墨烯在线创建工具 创建周期性体系的拓扑文件：以石墨烯为例 氧化石墨烯的结构与建模 石墨烯平面的卷曲与扭曲	graphene
pipistack	Pi-Pi堆积距离和堆积角度的计算	pipistack.tcl pipistack_linalg.tcl	ph2.zip
xpm2all	xpm文件处理脚本 xpm2all: xpm文件转换工具	xpm2all.bsh xpm2rgb.bat	ss.xpm gibbs.xpm
dssp2gp	使用xpm2all脚本计算蛋白二级结构演化及含量 xpm2all更新：二级结构绘制, 颜色方案 dssp数据绘图脚本dssp2gp	dssp2gp.bsh	dssp.dat
gmx_mmpbsa	gmx_mmpbsa使用说明 gmx_mmpbsa脚本更新：屏蔽效应与熵贡献 gmx_mmpbsa脚本更新：清理整理输出 gmx_mmpbsa更新：修正原子半径bug, 改用AMBRR PB4, 丙氨酸扫描CAS	gmx_mmpbsa.bsh	1ebz.zip
gmx_ir	使用GROMACS计算红外光谱 trr轨迹转换程序trr2all	gmx_ir.bsh
trr2all	使用GROMACS计算红外光谱 trr轨迹转换程序trr2all	trr2all.exe	spc216.zip
gmx_hbdat	GROMACS氢键分析工具hbond的使用及扩展 使用gnuplot绘制氢键数据的平行轴图	gmx_hbdat.bsh	hbdat_1crn.zip
remd_tgenerator	副本交换动力学T-REMD模拟的温度分布计算器	remd_tgenerator
xff	力场拟合工具xff开发杂记	xff	c6h6.fchk sf6.FChk
cagen	水溶液体系成笼分析程序cagen		cagen.zip
fitmol	README	FitMol.f90	ch4.xyz ch4_ch3oh.xyz
matchmol	分子结构匹配程序matchmol		matchmol.zip

Questions?

If you have any quesiotns about these tools, please let me know.

• Google Forum
• GitHub issues

gmxtools's Issues

Error: awk: cmd. line:154: (FILENAME=_pid.pdb FNR=115728) fatal: division by zero attempted

when i run:
./gmx_mmpbsa* -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -com Protein -pro receptor -lig ligand

I got an error:
1.4.1
running for Frame 1: _pid~0ns
awk: cmd. line:154: (FILENAME=_pid.pdb FNR=115728) fatal: division by zero attempted

Make vmd always at the top

Hi, thanks for your tool to make vmd automatically resize, is it possible to make it always at the top of the windows? It's annoying to click the 3 windows of vmd when I switched to another program and then switch back.

trr2all: Can't recognize gmx dump with trr2all Tool on Linux Cluster

Dear Dr. Li,

I encountered some issues while using your trr2all tool. Due to the significant computational load, I attempted to utilize the tool on a Linux cluster. It seems that I managed to run the .exe file using Wine, yet encountered errors during execution, as follows:

Can't recognize 'gmx_mpi dump -s /home/aczzq/ach-test.tpr -quiet ' as an internal or external command, or batch script.
At line 95 of file G:\Dropbox\prog\trr2all\trr2all.f90 (unit = 100, file = '/home/aczzq/ach-test.dmp')
Fortran runtime error: End of file

Error termination. Backtrace:

Could not print backtrace: executable file is not COFF
#0  0xffffffff
#1  0xffffffff
#2  0xffffffff
#3  0xffffffff
#4  0xffffffff
#5  0xffffffff
#6  0xffffffff
#7  0xffffffff
#8  0xffffffff
#9  0xffffffff
#10  0xffffffff
#11  0xffffffff
#12  0xffffffff
#13  0xffffffff
#14  0xffffffff
#15  0xffffffff
#16  0xffffffff

Given that your tool is compiled in .exe format, I find it challenging to pinpoint the source of the problem. I attempted to run the problematic command (gmx_mpi dump -s /home/aczzq/ach-test.tpr -quiet) in the terminal, and it executed without errors. Hence, I am uncertain about resolving this issue and would greatly appreciate your assistance amidst your busy schedule.

Thank you very much.

Illogical results

The values of bind free energr of protein-protein system are used to be positive, but change greatly after adjusting df slightly in the code. I have to say that the calculation result of this script is too illogical. And the author seems to have no intention of maintaining.

您好，我在使用gmx_ir的过程中遇到了如下问题，请问如何解决？

在“$gmx dump -quiet -s $tpr | awk -v ndx=$ndx -v grp=$grp -v atm=$atm >$chg '“步骤中，其输出的～atm.ndx中，只有[ System ]而并无其他数据且～chg.dat文件中无数据，vgro输出正常，请问这种情况应如何解决？

Awk error: division by zero attempted

Frame 1/13: _pid~25nsawk: cmd. line:205: (FILENAME=_pid.pdb FNR=122499) fatal: division by zero attempted
I have been encountering this with a new system. I have post processed the trajectory properly by -pbc whole and then used -pbc mol, and while running I'm encountering this error. Is this the problem with the system or that of my trajectory post processing?

gmx_MMPBSA: step3,awk: cmd. line:468: (FILENAME=_pid.pdb FNR=119376) warning: exp: argument 886.554 is out of range

Dear Dr. Li,
I have used gmx_MMPBSA.bsh to calculate the Gibes free energy. But the last step always reported error which is :awk: cmd. line:468: (FILENAME=_pid.pdb FNR=119376) warning: exp: argument 886.554 is out of range. I have checked the .tpr, .xtc, index.ndx file , and did not find any problems. I don't know how to solve this problem, please help me.

Awk error

Hello Dr. Li,
I have been encountering an error with the gmx_mmpbsa script where the script after running for a few frames say 140 or 150, the calculation stops with an error stating something like:
awk: cmd. line:183: (FILENAME=_pid.pdb FNR=3810933) fatal: attempt to access field -4
for which i searched through forums and found out that the error means that in the line number 3810933 which happens to be the last line the _pid.pdb (input file) it is trying to get the value of $(NF-4) which is failing as there is no 4th column/field in that particular line of my input file. The last line in my input file is ENDMDL.
PS: I have had all the trjconv functionalities as they were ending up in generating a lot of errors for me, hence I decided to create an index file containing only protein and ligand and thereafter dumped the trajectory with this index file and also dumped the _pid.pdb file with trjconv using the same index file.
Can you please help me figure out where I am getting it wrong ?
Moreover I have another question regarding calculating the MM(COU) part, do we need to input it in command line exclusively as -cou dh to calculate by Debye Huckel Screening or it does calculate it by default?

gmx_ir.bsh:This script is producing NAN results when calculating the infrared spectra of TIP4P water.

Dear Dr.Li, I tried the three-point water models spc, spce and the results were fine, but when calculating the infrared spectra of TIP4P water, all the data came out as NAN using gmx_ir.bsh.The version of GROMACS used is 2019.5. Below are some of the data computed.
@ title "Vibrational Power Spectrum"
@ xaxis label "\f{12}w\f{4} (cm\S-1\N)"
@ yaxis label "a.u."
@type xy
0 -nan
6.67128 -nan
13.3426 -nan
20.0138 -nan
26.6851 nan
33.3564 -nan
40.0277 -nan
46.699 -nan
53.3703 -nan
60.0415 -nan
66.7128 -nan
73.3841 -nan
80.0554 -nan
86.7267 -nan
93.3979 nan
100.069 -nan
106.741 -nan
113.412 -nan
120.083 -nan
126.754 -nan
133.426 -nan
140.097 -nan
146.768 -nan
153.439 -nan
160.111 nan
166.782 -nan