[gmx-users] CG-MD simulation of protein, always crash with protein

[XAvier Periole]

The representation of extended regions (b-sheets) is more stable using  
elastic
bonds than a dihedral angle because the flexibility of the force field  
makes possible
the occurrence of situations where the two bonds get aligned and  
therefore the
plan used to defined the dihedral can not be calculated and the  
program crashes.

But I am not sure that was your problem. You mentioned that the  
program was
stopping due to too many lincs warnings. Cycles (trp, phe, his) seemed  
to be the
cause.
Do you still have lincs warnings, may be less?

The other thing is that is your protein deforms as much as before,  
there is another
way to simulate you protein with  Martini:
http://md.chem.rug.nl/cgmartini/index.php/tools/118-end

XAvier.

On Apr 20, 2010, at 7:16 AM, Trang wrote:

> Elastic bonds did help the system survive. I'm not really understand  
> why do we need "more robust" bonds in this system. Does it mean that  
> there exists large forces that cause my system to blow up? Would you  
> mind giving an explanation?
>
> Thanks indeed for your taking time to help.
>
> Trang
>
>
> On Mon, Apr 19, 2010 at 4:26 PM, Martti Louhivuori <m.j.louhivuori at rug.nl 
> > wrote:
> On 19 Apr 2010, at 06:49, Trang wrote:
> The protein topo is too large, so I put it here. http://pastie.org/926617
>
> The protein topology is fine, but you could try also with elastic  
> bonds instead of dihedrals in the extended regions (--elastic  
> option). Elastic bonds are more robust than dihedrals, especially if  
> running with a larger timestep (30fs).
>
>
> Here is the system topology.
>
> ----------------------------
> #include "../martini_v2.1.itp"
> #include "../martini_v2.1_aminoacids.itp"
>
> The last line is unnecessary. Use it only when simulating single  
> aminoacids instead of a polypeptide.
>
>
> Minimized structure showed no close contact (with distance cutoff  
> 1.6, even to 1.9). Production run stopped at
>
> That's only 0.16-0.19nm, so overlap is still possible.
>
>
> step 175552 (5266.56 ps) with Segmentation fault, preceeded with a  
> lot of Lincs warnings (I set ring_bonds = "constraints").  This is  
> the mdp file, this file goes along with the system in vaccuum that  
> crashed. I'm not sure if
>
> What's different this time around? Last time you said you couldn't  
> run it even in vacuum.
>
> Sounds like you are just hitting statistical limits with your  
> combination of (extended) dihedrals + 30fs timestep. Use a smaller  
> timestep (20fs for example) or switch to local elastic bonds for the  
> beta-strands... and solvate the system (without overlap) so the  
> simulation makes some sense!
>
>
> -martti-
> --
> Post-doctoral research fellow
> Moleculaire Dynamica
> University of Groningen
> Nijenborgh 4, 9747AG Groningen, the Netherlands
> tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398
>
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