[gmx-users] Problem in energy calculation

[Gonzalez Fernandez, Cristina]

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,
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
http://www.thelemkullab.com

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