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Kalp Dimerization
- Tocci_89
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9 years 10 months ago #3908
by Tocci_89
Kalp Dimerization was created by Tocci_89
Hi everyone,
First of all thank you for the updated tutorial pages: now are really nice and more complete!
My question is about the point number 4. of the "Kalp" part of the protein tutorial:
"4. Double these previous boxes in one dimension (genconf) and rerun the simulations. Observe the different dimerization conformations (parallel or anti-parallel tilts). Note that more than one simulation might be required to observe both cases!"
I used genconf to double the box and it worked, but what about the .top file? I need to manually modify it and simply multiply the number of molecules and atoms or is there any other way to go on with the simulation? If so, I tried to, but grompp gives me "non-matching atom names" warning and they really don't match:
Warning: atom name 41 in dimero.top and dimer.gro does not match (BCQd - NC3)
Warning: atom name 42 in dimero.top and dimer.gro does not match (SCC3 - PO4)
Warning: atom name 43 in dimero.top and dimer.gro does not match (SCQd - GL1)
Warning: atom name 44 in dimero.top and dimer.gro does not match (BCP5 - GL2)
Warning: atom name 45 in dimero.top and dimer.gro does not match (SCC3 - C1A)
Warning: atom name 46 in dimero.top and dimer.gro does not match (SCQd - C2A)
Warning: atom name 47 in dimero.top and dimer.gro does not match (BCP4 - C3A)
Warning: atom name 48 in dimero.top and dimer.gro does not match (BHNd - C1B)
Warning: atom name 49 in dimero.top and dimer.gro does not match (SHAC1 - C2B)
Warning: atom name 50 in dimero.top and dimer.gro does not match (BHN0 - C3B)
Warning: atom name 51 in dimero.top and dimer.gro does not match (BHNd - NC3)
Warning: atom name 52 in dimero.top and dimer.gro does not match (SHAC1 - PO4)
Warning: atom name 53 in dimero.top and dimer.gro does not match (BHN0 - GL1)
Warning: atom name 54 in dimero.top and dimer.gro does not match (BHN0 - GL2)
Warning: atom name 55 in dimero.top and dimer.gro does not match (SHAC1 - C1A)
Warning: atom name 56 in dimero.top and dimer.gro does not match (BHC5 - C2A)
Warning: atom name 57 in dimero.top and dimer.gro does not match (BHN0 - C3A)
Warning: atom name 58 in dimero.top and dimer.gro does not match (SHAC1 - C1B)
Warning: atom name 59 in dimero.top and dimer.gro does not match (BHC5 - C2B)
Warning: atom name 60 in dimero.top and dimer.gro does not match (BHN0 - C3B)
(more than 20 non-matching atom names)
WARNING 1 file dimero.top, line 14]:
3240 non-matching atom names
atom names from dimero.top will be used
atom names from dimer.gro will be ignored
-NOTE: "dimero.top" is the new .top file with the manually added atoms
Hope my question is clear,
Kind regards
First of all thank you for the updated tutorial pages: now are really nice and more complete!
My question is about the point number 4. of the "Kalp" part of the protein tutorial:
"4. Double these previous boxes in one dimension (genconf) and rerun the simulations. Observe the different dimerization conformations (parallel or anti-parallel tilts). Note that more than one simulation might be required to observe both cases!"
I used genconf to double the box and it worked, but what about the .top file? I need to manually modify it and simply multiply the number of molecules and atoms or is there any other way to go on with the simulation? If so, I tried to, but grompp gives me "non-matching atom names" warning and they really don't match:
Warning: atom name 41 in dimero.top and dimer.gro does not match (BCQd - NC3)
Warning: atom name 42 in dimero.top and dimer.gro does not match (SCC3 - PO4)
Warning: atom name 43 in dimero.top and dimer.gro does not match (SCQd - GL1)
Warning: atom name 44 in dimero.top and dimer.gro does not match (BCP5 - GL2)
Warning: atom name 45 in dimero.top and dimer.gro does not match (SCC3 - C1A)
Warning: atom name 46 in dimero.top and dimer.gro does not match (SCQd - C2A)
Warning: atom name 47 in dimero.top and dimer.gro does not match (BCP4 - C3A)
Warning: atom name 48 in dimero.top and dimer.gro does not match (BHNd - C1B)
Warning: atom name 49 in dimero.top and dimer.gro does not match (SHAC1 - C2B)
Warning: atom name 50 in dimero.top and dimer.gro does not match (BHN0 - C3B)
Warning: atom name 51 in dimero.top and dimer.gro does not match (BHNd - NC3)
Warning: atom name 52 in dimero.top and dimer.gro does not match (SHAC1 - PO4)
Warning: atom name 53 in dimero.top and dimer.gro does not match (BHN0 - GL1)
Warning: atom name 54 in dimero.top and dimer.gro does not match (BHN0 - GL2)
Warning: atom name 55 in dimero.top and dimer.gro does not match (SHAC1 - C1A)
Warning: atom name 56 in dimero.top and dimer.gro does not match (BHC5 - C2A)
Warning: atom name 57 in dimero.top and dimer.gro does not match (BHN0 - C3A)
Warning: atom name 58 in dimero.top and dimer.gro does not match (SHAC1 - C1B)
Warning: atom name 59 in dimero.top and dimer.gro does not match (BHC5 - C2B)
Warning: atom name 60 in dimero.top and dimer.gro does not match (BHN0 - C3B)
(more than 20 non-matching atom names)
WARNING 1 file dimero.top, line 14]:
3240 non-matching atom names
atom names from dimero.top will be used
atom names from dimer.gro will be ignored
-NOTE: "dimero.top" is the new .top file with the manually added atoms
Hope my question is clear,
Kind regards
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- Clement
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9 years 10 months ago - 9 years 10 months ago #3909
by Clement
Replied by Clement on topic Kalp Dimerization
You indeed have to modify it by hand. If you multiply the box by 2, you have to multiply your topology accordingly. From the following (fake) system topology:
You would need to modify to reflect your modification (here just double the number of boxes in one dimension):
Careful about the order in which you list your molecules in your topology! The "non-matching names" warnings you get in your case is coming from that...
[...]
KALP 4
DPPC 128
DOPC 96
[...]You would need to modify to reflect your modification (here just double the number of boxes in one dimension):
[...]
KALP 4
DPPC 128
DOPC 96
KALP 4
DPPC 128
DOPC 96
[...]Careful about the order in which you list your molecules in your topology! The "non-matching names" warnings you get in your case is coming from that...
Last edit: 9 years 10 months ago by Clement.
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- Tocci_89
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9 years 10 months ago #3910
by Tocci_89
Replied by Tocci_89 on topic Kalp Dimerization
Thank you for answering so quick!
It worked!
Now just another question: mdrun is running, is it supposed to see at the end dimerization or I need a longer simulation?
Note that I'm using dynamic.mdp as running parameters.
It worked!
Now just another question: mdrun is running, is it supposed to see at the end dimerization or I need a longer simulation?
Note that I'm using dynamic.mdp as running parameters.
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- Clement
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9 years 10 months ago #3911
by Clement
Replied by Clement on topic Kalp Dimerization
It's a stochastic event! It might or might not happen within the simulation time you requested (nsteps in the .mdp file). If not, just increase this number or put it at -1.
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9 years 10 months ago #3912
by Tocci_89
Replied by Tocci_89 on topic Kalp Dimerization
Ok! I'll see what happens and I'll try so if nothing happens.
Thank you so much one more time!
Kind Regards
Thank you so much one more time!
Kind Regards
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