[gmx-users] Running simulation differences
Justin Lemkul
jalemkul at vt.edu
Fri Dec 21 14:40:40 CET 2018
On Thu, Dec 20, 2018 at 2:58 PM Gonzalez Fernandez, Cristina <
cristina.gonzalezfdez at unican.es> wrote:
>
> 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).
>
>
What are your settings in NAMD? If you're getting a different result then
either the input settings for the energy function are different or there is
some difference in the system's topology.
-Justin
>
> 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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--
==========================================
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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