Nmtraj issue

User discussions
1

GROMACS version: 2023.3
GROMACS modification: No
Hi,

I am working with a single ethanol molecule using a custom forcefield. I did an mdrun using ‘integrator=nm’ to obtain the Hessian matrix at the energy minimum. Then I used nmeig to obtain the eigenvectors and eigenfrequencies. I am now trying to use gmx nmtraj to produce a .trr file containing a movie of a normal mode motion. I used the command

gmx nmtraj -s nm.tpr -v eigenvec.trr

, and got the following error message:

Program: gmx nmtraj, version 2023.3-Homebrew
Source file: src/gromacs/utility/strconvert.cpp (line 88)
Function: int gmx::intFromString(const char*)

Error in user input:
Invalid value: ‘0.0’; expected an integer

Can someone tell me how to fix this error?
Thanks!

2

Hi,

As a workaround, try adding -phases 0 option. This is anyway the default, but it seems there is a bug in GROMACS with how this default is handled.

3

Thanks!

4

Thanks again for reporting the problem. It will be fixed in the upcoming 2024.1 release.