[gmx-users] problem

[Alex]

Hi

On Sat, May 5, 2018 at 1:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I don't know of any forcefield that uses such nonbonded cutoffs, but that
> should probably not of itself lead to instability. It will just be harder
> to convince your reviewers that your simulation models reality.
>
I do not understand what you mean, you mean the 1.3 nm for the rcoulomb and
rvdw is not a good choice?
Thanks.
Alex

>
> Mark
>
> On Sat, May 5, 2018, 12:35 Alex <alexanderwien2k at gmail.com> wrote:
>
> > Dear all,
> > In my NVT production simulation, I get several LINCS warning in step
> number
> > 2600 which crashes the simulation. I know the reason might be the
> > instability or not being well equilibrated system, but the point is that
> > the below equilibration steps have been conducted successfully before the
> > NVT production.
> >
> > 2 minimisation,
> > 1 NVT equilibration at T =600 (1.5 ns)
> > 1 NpT equilibration 3.5 ns
> > 1 NVT equilibration at T =298.15 (1 ns)
> > 1 NpT equilibration 7 ns
> > -----------
> > Below is my prd.mdp file and the link is my log files, I would be so
> > appreciated if you could let me know what might be the reason;
> >
> > https://drive.google.com/open?id=11BeWr6TToh2vJhtWARTJKVeBInt5CSlt
> >
> > https://drive.google.com/open?id=1Ijg8u9ywvFqXZcybRPjnvMxGOy7OI3FK
> > ------------------------
> > title                    = GPS
> > integrator               = md
> > dt                       = 0.002     ; 2 fs
> > nsteps                   = 6000000   ;12 ns
> > xtc-precision            = 2000
> > nstlist                  = 40
> >
> > nstxout                  = 1000
> > nstvout                  = 1000
> > nstfout                  = 0
> > nstlog                   = 2000
> > nstcalcenergy            = 100
> > nstenergy                = 200
> > nstxout-compressed       = 500
> >
> > continuation             = yes
> > gen-vel                  = no
> > ;gen-temp                 = 298.15
> > ;gen-seed                 = 173529
> >
> > constraint-algorithm     = lincs
> > constraints              = h-bonds
> >
> > cutoff-scheme            = Verlet
> >
> > coulombtype              = PME
> > rcoulomb                 = 1.3
> >
> > vdwtype                  = Cut-off
> > rvdw                     = 1.3
> > DispCorr                 = EnerPres
> >
> > tcoupl                   = v-rescale    ;;berendsen  ;Nose-Hoover
> > tc-grps                  =T1GPS
> > tau-t                    = 1.0
> > ref-t                    = 298.15
> > nhchainlength            = 1
> > pbc                      = xyz
> >
> > pcoupl                   = no           ;berendsen
> > ;;Parrinello-Rahman
> > ;Pcoupltype               = isotropic          ;semiisotropic
> > ;tau_p                    = 2.5
> > ;compressibility          = 4.46e-5            ;0.0 4.46e-5
> > ;ref_p                    = 1.0                ;1.0 1.0
> > refcoord-scaling         = com
> >
> > Thank you.
> > Regards,
> > Alex
> > --
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