[gmx-users] Error in NVT equilibration

[Gonzalez Fernandez, Cristina]

Hi Justin,


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:

;Simulated annealing

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,


C.


________________________________
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:
> Hi,
>
>
> 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
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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