[gmx-users] Protein in SDS, GROMOS96 ff, MD crash - SDS molecule comes apart, LINCS error

Venky venky.agas at gmail.com
Wed Apr 25 20:10:45 CEST 2007


Thanks Tsjerk,

I am rerunning the simulation with SDS+SOL+IONS in a single tcoupl group.
I was trying to anneal because, I suspected huge velocities on the atoms due
to a "high starting temperature", well not high enough to be worried and I
had done a NVT equilibration already, so shouldn't cause any problems, but I
just wanted to be sure.
I am running the SDS simulations with water simultaneously... haven't
checked its properties yet.

Venky

On 4/25/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> Hi Venky,
>
> On 4/25/07, Venky Krishna <venky.agas at gmail.com> wrote:
> > Hi gmx-users,
> >
> > System Setup:
>
> Looks good
>
> >
> > Problem:
>
> Did you check the PRODRG2 derived parameters? Run through the molecule
> yourself (draw it!). Check the atom, bond, etc. types. Also, run a
> simulation of only SDS (with water) to check the properties, like the
> area per lipid, etc.
>
> >
> > Parameters:
>
> Won't go through all this... (but thanks for adding it..., makes it a
> good mail..., I'm just being lazy).
>
> > and here are my relevant MD mdp parameters.
>
> > tc-grps                  = Protein      SDS     SOL     Na+     Cl-
> > tau-t                    = 0.5          0.5     0.5     0.5     0.5
> > ref-t                     = 300          300     300     300     300
>
> This is BAD BAD BAD! We just dealt with this issue a few times in the
> past few weeks! It may be the cause of your problem, and you should
> fix it and rerun the simulation, before turning back to the list.
> Merge your sodium and chloride with the solvent, so you have three
> reasonably large groups to couple to the heat bath. Check the archives
> on this one.
>
> > ; SIMULATED ANNEALING
> > ; Type of annealing for each temperature group (no/single/periodic)
> > annealing                = single single single single single
> > ; Number of time points to use for specifying annealing in each group
> > annealing_npoints        = 2 2 2 2 2
> > ; List of times at the annealing points for each group
> > annealing_time           = 0 20 0 20 0 20 0 20 0 20
> > ; Temp. at each annealing point, for each group.
> > annealing_temp           = 0 300 0 300 0 300 0 300 0 300
>
> Is there any specific reason for annealing here? You didn't mention it
> in your setup.
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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-- 
Venks

~ You will become rich and famous, unless you don't.
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