[gmx-users] Problem in energy calculation

Gonzalez Fernandez, Cristina cristina.gonzalezfdez at unican.es
Thu Oct 4 17:30:58 CEST 2018

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?

Thank you for all your help,

-----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 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


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