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

[Tsjerk Wassenaar]

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