jerkwin/gmxtools

tools for GROMACS

gmxtools's Issues

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.

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？

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

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.

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?

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.

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.

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

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?