[gmx-users] Problem in energy calculation

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 16:58:08 CEST 2018

On 10/4/18 10:42 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Justin,
> Thank you for your suggestions. I have a doubt regarding the groups generation. I have created the two groups I need as:
> gmx make_ndx -f em.gro -o index1.ndx
>> 1
>> q
> and
> gmx make_ndx -f em.gro -o index2.ndx
>> 11
>> q
> However, I can only introduce one .ndx file in the gmx grompp option, since if I try introducing both an error appears: Invalid command-line options. In command-line option -n. Too many values.
> How can I solve it?

You're using default groups, you're not creating anything new. An index 
*file* contains as many *groups* as you want, so you never need two files.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list