[gmx-users] Protein in SDS, GROMOS96 ff, MD crash - SDS molecule comes apart, LINCS error
venky.agas at gmail.com
Wed Apr 25 20:10:45 CEST 2007
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.
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.
> 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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