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

Wed, 25 Apr 2007 13:50:02 -0700 

Thanks again Tsjerk,

I am making the required changes.

Venky

On Apr 25, 2007, at 1:06 PM, Tsjerk Wassenaar wrote:


Hi Venky,

Now I'm not sure whether putting the SDS and the solvent (SOL+Ions)
together is the best idea. The temperature coupling groups have to do
with the different behaviour (speed) in dissipation of heat. If
there's a difference between two parts of your system (which I suspect
there is in the case of SDS and water) and they're coupled to the same
bath, this means that one part may accumulate heat at the cost of the
other. Averaged over the subsystems the temperature will be right, but
for each of the parts it's wrong. Maybe you're better of coupling the
lipids with the peptide.

Cheers,

Tsjerk

On 4/25/07, Venky <[EMAIL PROTECTED]> wrote:

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 < [EMAIL PROTECTED]> wrote:
>
> Hi Venky,
>
> On 4/25/07, Venky Krishna < [EMAIL PROTECTED]> 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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--
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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