[gmx-users] Error in NVT equilibration
Gonzalez Fernandez, Cristina
cristina.gonzalezfdez at unican.es
Wed Sep 19 12:14:34 CEST 2018
I’ve been looking for the non-bonded setting parameters for the GROMOS force field. I have found that for this force field coulmb_modifier and vdw_modifier = Potential-shift-Verlet. I have changed this in the .mdp file, but I don’t have seen more differences, Is it correct? Is it enough to change the columb and vdw modifier option?. I obtain the same error when running the equilibration.
I have tryied to use the default GMX values for dt (0,002) and nsteps (50000) because they are so different to the ones I have proposed (0,015 and 6667 respectively) and the nvt equilibration runs. My values derive from the annealing I am trying, and with the default values the annealing is not fulfilled since the temperature doesn’t start in the first annealing temperature.
I need to increase the temperature from 278 to 298K with a rate of 0,298 K every time step for 1 ps. I checked your previous posts and use annealing for that purpose. From the rate 0,298K/step and knowing that I need to increase 20 K de temperature, I calculate the requied number of steps and from this value and 1 ps I found that dt should be 0,015 ps. From this dt, as I considered a total equilibration time of 100 ps, I calculated nsteps (6667).
The annealing settings are:
annealing = single
annealing_npoints = 2
annealing_time = 0 1
annealing_temp = 278 298
How can I satisfy the 0,298K increase during 1 ps until 298K while running the equilibration?
Thank you for all your help,
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 <jalemkul at vt.edu>
Enviado: martes, 18 de septiembre de 2018 13:37:24
Para: gmx-users at gromacs.org
Asunto: Re: [gmx-users] Error in NVT equilibration
On 9/18/18 5:33 AM, Gonzalez Fernandez, Cristina wrote:
> As I am using the GROMOS froce field, I constrained all bonds as suggested. However, I obtained the same error.
> I copy the .mdp file in case there are errors and you can help me to find them:
> title = Lipid NVT equilibration
> define = -DPOSRES ; position restrain the Lipid
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 6667 ; 2 * 50000 = 100 ps
> dt = 0.015 ; 2 fs
> ; Output control
> nstxout = 500 ; save coordinates every 1.0 ps
> nstvout = 500 ; save velocities every 1.0 ps
> nstenergy = 500 ; save energies every 1.0 ps
> nstlog = 500 ; update log file every 1.0 ps
> ; Bond parameters
> continuation = no ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; bonds involving H are constrained
> ;shake_tol = 0.0001
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Nonbonded settings
> cutoff-scheme = Verlet ; Buffered neighbor searching
> ns_type = grid ; search neighboring grid cells
> nstlist = 10 ; 20 fs, largely irrelevant with Verlet
> rlist = 1.4
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> DispCorr = EnerPres ; account for cut-off vdW scheme
> vdwtype = Cut-off
> vdw_modifier = Force-switch
You're using nonbonded settings for the CHARMM force field, so you need
to correct these settings to use the proper GROMOS values.
Beyond that, follow
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