- Posts: 91
Tutorial on Sugars
- vainikka
-
- Offline
- Admin
Less
More
3 years 1 month 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.
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.
Please Log in or Create an account to join the conversation.
- cm
-
- Offline
- Senior Boarder
Less
More
- Posts: 73
3 years 1 month 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.
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.
Please Log in or Create an account to join the conversation.
- vainikka
-
- Offline
- Admin
Less
More
- Posts: 91
3 years 1 month 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?
Please Log in or Create an account to join the conversation.
- cm
-
- Offline
- Senior Boarder
Less
More
- Posts: 73
3 years 1 month 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.
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.
Please Log in or Create an account to join the conversation.
- vainikka
-
- Offline
- Admin
Less
More
- Posts: 91
3 years 1 month 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?
Please Log in or Create an account to join the conversation.
- cm
-
- Offline
- Senior Boarder
Less
More
- Posts: 73
3 years 1 month 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
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
Please Log in or Create an account to join the conversation.
- cm
-
- Offline
- Senior Boarder
Less
More
- Posts: 73
3 years 1 month 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.
Please Log in or Create an account to join the conversation.
- cm
-
- Offline
- Senior Boarder
Less
More
- Posts: 73
3 years 3 weeks ago #8914
by cm
Replied by cm on topic Tutorial on Sugars
can you please share the mdp file and the steps and commands.
Please Log in or Create an account to join the conversation.
Time to create page: 0.109 seconds