normal Tutorial on Sugars

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3 years 3 months ago #8884 by vainikka
Replied by vainikka on topic Tutorial on Sugars
Without any further details about your system it is going to be impossible to say what's going wrong. I just finished testing a system with 100 TREH, 200 GLUC and 500 W molecules, and it works just fine (at least I can run dt=20fs for some tens of nanoseconds with no issues).

You can find the system here, maybe it will help you get forward:
unishare.nl/index.php/s/d9pQgWf8ZaQF62t

As for the concentration: You'll need to take in to account that a normal water bead represents 4 water molecules, but other than that it is just the same as with AA systems.

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3 years 3 months ago #8885 by cm
Replied by cm on topic Tutorial on Sugars
thank you so much for your quick reply.
My system consist of two proteins, water, ion and carbohydrate.
1. I have placed two cg proteins at a certain distance from each other and minimized in vaccum.
2. then solvated the system.
3. next minimized the system by including martini-ion.itp and martini-sugar.itp.

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3 years 3 months ago #8886 by vainikka
Replied by vainikka on topic Tutorial on Sugars
How did you obtain the parameters for the proteins, with martinize? Have you tried running short equilibration simulations on the proteins alone?

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3 years 3 months ago #8887 by cm
Replied by cm on topic Tutorial on Sugars
I have obtained the coarse grained parameter of proteins by martinized.py script.
I have already made a system with two proteins, waters and ions (all in cg), which is already run at 20 fs time step for 10 micro second following this tutorial:
cgmartini.nl/index.php/tutorials-general...n-gmx5/proteins-gmx5 .

But this time i want to incorporate trehalose (1 (M)).
In both case i followed the same steps, but to incorporate trehalose i just included martini-sugar.itp in the top file during the minimization steps.

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3 years 3 months ago #8890 by vainikka
Replied by vainikka on topic Tutorial on Sugars
Then your issue is most likely with the top file. Can you copy paste it here?

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3 years 3 months ago #8892 by cm
Replied by cm on topic Tutorial on Sugars
sorry for replying late, i was out of station.
the top file is
#include "martini_v2.2.itp"
#include "Protein_A.itp"
#include "martini_v2.0_sugars.itp"
#include "martini_v2.0_ions.itp"
[system]
;Martini system from 5B1F2.PDB in water

[molecules]
;name number
Protein_A 2
W 10177
TREH 50
CL- 16

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3 years 2 months ago #8903 by cm
Replied by cm on topic Tutorial on Sugars
am i doing anything wrong. Could you please suggest me anything to solve this problem.

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3 years 2 months ago #8914 by cm
Replied by cm on topic Tutorial on Sugars
can you please share the mdp file and the steps and commands.

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