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

[Venky Krishna]

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 <venky.agas at gmail.com> 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 < 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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>
>
> -- 
> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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