[gmx-users] problem

[Mark Abraham]

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.

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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