[gmx-users] Running simulation differences
Gonzalez Fernandez, Cristina
cristina.gonzalezfdez at unican.es
Thu Dec 20 20:58:01 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.
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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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