[gmx-users] Problem in energy calculation

[Gonzalez Fernandez, Cristina]

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?

Thank you again,
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 15:15
Para: gmx-users at gromacs.org
Asunto: Re: [gmx-users] Problem in energy calculation



On 10/3/18 7:08 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
>
>
>
>
>
> I want to calculate the van der waals and electrostatic interaction energy  between a lipid and water. For that purpose, and following the gromacs tutorials I have performed the following steps:
>
>
>
>    *   I have include: energygrps = Other Water  in the .mdp file to be used in the energy minimization. I copy the .mdp file:
>
>
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator    = cg        ; Algorithm (steep = steepest descent minimization)
> emtol        = 1000.0      ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep          = 0.01      ; Energy step size
> nsteps        = 50000          ; Maximum number of (minimization) steps to perform
> energygrps      = Other Water
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist            = 1            ; Frequency to update the neighbor list and long range forces
> cutoff-scheme       = Verlet
> ns_type            = grid        ; Method to determine neighbor list (simple, grid)
> coulombtype        = PME        ; Treatment of long range electrostatic interactions
> rcoulomb        = 1.4        ; Short-range electrostatic cut-off
> rvdw            = 1.4        ; Short-range Van der Waals cut-off
> pbc            = xyz         ; Periodic Boundary Conditions (yes/no)
>
>
>
>
>
>    *   From the output of the minimization (em.gro) I have grouped Other (lipid) and Water:
>
> gmx make_ndx -f em.gro -o index.ndx
>
>> 1 | 11
>> q

You don't need a merged group. You need two groups for which the interaction energy will be computed.

>             gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx 
> -o nvt.tpr
>
>             nohhup gmx mdrun -deffnm nvt &
>
>
>
>
>
>    *   Finally, I used gmx energy to determine the electrostatic and van der waals energies. However, when I select 42 (Coul-SR: Other-Water) and 43 (LJ-SR: Other-Water) the results for both energies are 0 KJ/mol.

If you're running on a GPU and a pre-2018 version, this is exactly what you should expect. energygrps should only be used as a post-processing analysis, on CPU hardware. They are unnecessary for the actual simulation and are not compatible with GPUs.

-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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