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

[Trang]

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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