[gmx-users] Problem in energy calculation

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 17:32:37 CEST 2018

On 10/4/18 11:30 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Justin,
> Following your previous email, I have used only index1.ndx in the grompp. But after running the equilibration, the options of gmx energy don't include  Coul-SR: Other-Water or LJ-SR: Other-Water, so I cannot determine the interaction energy of the lipid and water.
> How can I determine these energies?

If the energy terms weren't written, then you didn't request them in 
your .mdp using energygrps.

Again, you don't need to do this *during* the run, you should treat 
interaction energy analysis (which may not even be a meaningful 
quantity) as post-processing. You can generate a new .tpr file with the 
desired energygrps and use mdrun -rerun with the new .tpr file to get 
the interaction energies.


> Thank you for all your help,
> C.
> -----Mensaje original-----
> De: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> En nombre de Justin Lemkul
> Enviado el: jueves, 4 de octubre de 2018 16:58
> Para: gmx-users at gromacs.org
> Asunto: Re: [gmx-users] Problem in energy calculation
> 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


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