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Protein + dsDNA complex errors
- bqAlvii
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1 year 2 months ago #9584
by bqAlvii
Protein + dsDNA complex errors was created by bqAlvii
Hi community!
I have some problems trying to performing Martini MD simulation of DNA + Protein complex, and im looking for some help or advice :C.
My system its composed by :
1 protein -> 630 residues
1 dsDNA -> 69 nucleotides
Water, AntiFreeze Water, Salt.
In a box of 30x30x30. Both, Protein and dsDNA are placed really distant (that's the reason why the box its so big ...), the idea is evaluate in long simulation time autonomous biding between protein and dsDNA, dt = 0.001, pressure = 3e-4.
Through martini simulation. Can pass through minimization step but couldn't pass NVT or NPT equilibration due some error and abnormal "freezing" of process. I followed the
In NVT i get these errors :
While running the grompp i get a Segmentation fault (core dumped) error.
Abnormal Freezing of terminal. The terminal get stuck at random step (could be at any step ... 100, 2000, 10000 etc).
In NPT i get this error :
While running the grompp i get "Warning: pressure scaling more than 1%, mu: 0.98803 0.98803 0.98803"
Am i doing something wrong?, i can upload NVT & NPT files if is needed.
:c
I have some problems trying to performing Martini MD simulation of DNA + Protein complex, and im looking for some help or advice :C.
My system its composed by :
1 protein -> 630 residues
1 dsDNA -> 69 nucleotides
Water, AntiFreeze Water, Salt.
In a box of 30x30x30. Both, Protein and dsDNA are placed really distant (that's the reason why the box its so big ...), the idea is evaluate in long simulation time autonomous biding between protein and dsDNA, dt = 0.001, pressure = 3e-4.
Through martini simulation. Can pass through minimization step but couldn't pass NVT or NPT equilibration due some error and abnormal "freezing" of process. I followed the
In NVT i get these errors :
While running the grompp i get a Segmentation fault (core dumped) error.
Abnormal Freezing of terminal. The terminal get stuck at random step (could be at any step ... 100, 2000, 10000 etc).
In NPT i get this error :
While running the grompp i get "Warning: pressure scaling more than 1%, mu: 0.98803 0.98803 0.98803"
Am i doing something wrong?, i can upload NVT & NPT files if is needed.
:c
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