[gmx-users] Problem in energy calculation
Gonzalez Fernandez, Cristina
cristina.gonzalezfdez at unican.es
Thu Oct 4 16:42:09 CEST 2018
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
gmx make_ndx -f em.gro -o index2.ndx
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,
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
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users