[gmx-users] RV: Running simulation differences

Gonzalez Fernandez, Cristina cristina.gonzalezfdez at unican.es
Thu Dec 20 21:45:23 CET 2018


Hi Justin,


Sorry for the misunderstanding. I am simulating the interaction of a lipid with water. I obtain practically the same value for the coulomb interaction energy, but I am not able to get a value for the van der waals energy close to the published one (although I have used the same settings than the ones used in the article). Therefore, I checked tha GMX manual and I tried to modified the settings that affect the van der waals energy in order to get a better value: vdwtype, vdw-modifier, rvdw and DispCorr (as I am using GROMOS96 FF I don't consider rvdw-switch).


This is the .mdp file:


title                = Lipid A  simulation
; Run parameters
integrator          = md        ; leap-frog integrator
nsteps                = 5500000        ; 2 * 50000 = 100 ps
dt                    = 0.002        ; 2 fs
; Output control
nstxout                = 5000        ; save coordinates every 1.0 ps
nstvout                 = 5000        ; save velocities every 1.0 ps
nstenergy           = 5000        ; save energies every 1.0 ps
nstlog                = 5000        ; update log file every 1.0 ps
nstxtcout               = 5000
xtc-grps                = System
; Bond parameters
continuation            = yes        ; restarting after NVT
constraint_algorithm    = lincs        ; holonomic constraints
constraints            = all-bonds    ; all bonds (even heavy atom-H bonds) constrained
lincs_iter            = 1            ; accuracy of LINCS
lincs_order            = 4            ; also related to accuracy
; Nonbonded settings
cutoff-scheme           = Verlet
ns_type                = grid        ; search neighboring grid cells
nstlist                = 5        ; 20 fs, largely irrelevant with Verlet
rcoulomb            = 1.4        ; short-range electrostatic cutoff (in nm)
rvdw                = 1.4        ; short-range van der Waals cutoff (in nm)
rlist                   = 1.41
vdwtype                 = Cut-off
vdw_modifier            = None
verlet-buffer-drift     = -1
; Electrostatics
coulombtype            = Reaction-Field    ; Particle Mesh Ewald for long-range electrostatics
epsilon_rf              = 61
; Temperature coupling is on
tcoupl           = nose-hoover    ; modified Berendsen thermostat
tc-grps                = System    ; two coupling groups - more accurate
tau_t                = 0.2               ; time constant, in ps
ref_t                = 298                ; reference temperature, one for each group, in K
; Pressure coupling is oN
pcoupl                  = Parrinello-Rahman         ; Pressure coupling on in NPT
pcoupltype              = isotropic                 ; uniform scaling of box vectors
tau_p                   = 0.5                       ; time constant, in ps
ref_p                   = 1.0                       ; reference pressure, in bar
compressibility         = 4.5e-5                    ; isothermal compressibility of water, bar^-1
;refcoord_scaling        = com
; Periodic boundary conditions
pbc                = xyz            ; 3-D PBC
;Dispersion correction
;DispCorr            = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel                 = no        ; assign velocities from Maxwell distribution
;gen_temp            = 278        ; temperature for Maxwell distribution
;gen_seed            = -1        ; generate a random seed

I would greatly appreciate if you could help me, because I don't know what else I can do,

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: jueves, 20 de diciembre de 2018 19:52:20
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] Running simulation differences

On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina <
cristina.gonzalezfdez at unican.es> wrote:

> Hi Justin,
>
>
> Do you think that the difference between a value of -280 ± 37 kj/mol
> obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable?
>
>
As I said before, no, a massive difference like that, outside the error
bars, is not acceptable.

If you want more useful advice, you'll have to tell us exactly what you're
doing and trying to compare.

-Justin


>
> Thank you so much 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 diciembre de 2018 15:34:07
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Running simulation differences
>
> On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina <
> cristina.gonzalezfdez at unican.es> wrote:
>
> > Hi again Justin,
> >
> > I've been thinking about the normal variability between MD simulations
> you
> > commented. I am simulating the interaction of a lipid with water, but the
> > van der waals energy value that I obtain (-257.25  ± 35.86 kj/mol) for me
> > is considerably different from the published value (-361 kj/mol).
> However,
> > according to your email maybe these values can be considered similar. Do
> > you think my value and the published one are similar? How can I reduced
> the
> > error of the results because my value correspond to a long
>
>
> I would not call those values similar at all. The two quantities you posted
> before were within error of one another; those are similar. A difference of
> over 100 kJ/mol, outside error, is enormous. You need to evaluate what
> you're doing because in that case, I suspect something is inconsistent
> between what is published and what you're doing.
>
>
> > simulation (60 ns)? Could you recommend me a paper where is stated the
> > common deviations/errors that are acceptable to a simulation result?
> >
>
> There is none to my knowledge, and certainly can't be generalized.
> Different quantities have different tolerances. Different software may
> produce somewhat different results, as well.
>
> Also I wouldn't consider 60 ns long, by any means :)
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
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--

==========================================

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com


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