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cg mapping
- syahidah
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13 years 2 months ago #544
by syahidah
cg mapping was created by syahidah
greeting everyone,
i'm syahidah from universiti putra malaysia.fyi,my project is about the coarse grained simulation by using gromacs.so, i need to do the coarse graining for the molecules that i will use in the simulation.(i'm doing CGMD for surfactant-micelle formation).however, i don't know how to do the correct 4 to 1 mapping procedure.may I know whether there is any software to do the mapping and if there is any paper that provides the mapping process from the scratch.i do really need it because i am so new with CGMD.
thank you,
best,
syahida.
i'm syahidah from universiti putra malaysia.fyi,my project is about the coarse grained simulation by using gromacs.so, i need to do the coarse graining for the molecules that i will use in the simulation.(i'm doing CGMD for surfactant-micelle formation).however, i don't know how to do the correct 4 to 1 mapping procedure.may I know whether there is any software to do the mapping and if there is any paper that provides the mapping process from the scratch.i do really need it because i am so new with CGMD.
thank you,
best,
syahida.
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- xavier
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13 years 2 months ago #546
by xavier
You should have a look at the protein and sugar paper for exemples of mapping molecules and the type of data you'd like to reproduce. You'll find this papers on the main page of the website.
XAvier.
Replied by xavier on topic cg mapping
There is no script that would do the mapping for you. It is something you have to do manually as it is extremely depending on the molecule you like to coarse grain, the data you have at hand to parameterize, and the complexity of the molecule.syahidah wrote: greeting everyone,
i'm syahidah from universiti putra malaysia.fyi,my project is about the coarse grained simulation by using gromacs.so, i need to do the coarse graining for the molecules that i will use in the simulation.(i'm doing CGMD for surfactant-micelle formation).however, i don't know how to do the correct 4 to 1 mapping procedure.may I know whether there is any software to do the mapping and if there is any paper that provides the mapping process from the scratch.i do really need it because i am so new with CGMD.
thank you,
best,
syahida.
You should have a look at the protein and sugar paper for exemples of mapping molecules and the type of data you'd like to reproduce. You'll find this papers on the main page of the website.
XAvier.
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13 years 2 months ago #606
by syahidah
Replied by syahidah on topic cg mapping
i'm so sorry..but may i know how to do the coarse grained structure?i've read in an article that we can do the coarse graining by using vmd.however,the tutorial is quite simple for me.i rally need help to do this.i'm wondering how to prepare the coarse grained structure.
begging for help,
tahnk you,
best,
syahida
begging for help,
tahnk you,
best,
syahida
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13 years 2 months ago #607
by syahidah
Replied by syahidah on topic cg mapping
fyi,i want to do the coarse grained structure for surfactant phosphatidylcholine. i know the formula to do the mapping,(Q,P,C..)however,i don't know how to prepare it to be used in simulation.
thank you,
syahida
thank you,
syahida
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13 years 2 months ago #608
by syahidah
Replied by syahidah on topic cg mapping
i've tried to use the "atom2cg_v2.1.awk" which is provided in this page,however,it worked for protein,amino acid only and it didn't work for surfactant molecule and other structure other than proteins.
best,
syahida
best,
syahida
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- xavier
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13 years 2 months ago #609
by xavier
Indeed atom2cg_v2.1.awk works only for proteins.
To make things clear, there are two things:
1- the topology of your molecule that should be defining the atoms/bond/angles etc. This you have already I assume
2- you need a structure file containing the coordinate of your CG beads. There is not such a script that would generate it for you. One may reason is that if you develop a new molecule the script would not know how to deal with it!
A solution for you is probably to choose from an atomistic structure file atoms close to the COM of the groups defining the CG-beads. Then a minimization should fix all the inexactitudes of the positions of the beads.
XAvier.
Replied by xavier on topic cg mapping
syahidah wrote: i've tried to use the "atom2cg_v2.1.awk" which is provided in this page,however,it worked for protein,amino acid only and it didn't work for surfactant molecule and other structure other than proteins.
best,
syahida
Indeed atom2cg_v2.1.awk works only for proteins.
To make things clear, there are two things:
1- the topology of your molecule that should be defining the atoms/bond/angles etc. This you have already I assume
2- you need a structure file containing the coordinate of your CG beads. There is not such a script that would generate it for you. One may reason is that if you develop a new molecule the script would not know how to deal with it!
A solution for you is probably to choose from an atomistic structure file atoms close to the COM of the groups defining the CG-beads. Then a minimization should fix all the inexactitudes of the positions of the beads.
XAvier.
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12 years 6 months ago #798
by syahidah
Replied by syahidah on topic cg mapping
dear sir,
do wee need to have .xtc file from our all-atom/ united atom simulation to complete the coarse graining?
it is because,in the tutorial,it gives 2 commands in coarse-graining part :
which is the first one is to produce cg.gro
-> g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
the second one is to produce fg2cg.xtc
-> g_fg2cg -pfg fg.top -pcg cg.top -c fg.xtc -n 1 -o fg2cg.xtc
what if we don't have fg,xtc from aa/ua simulation?
furthermore, i've tried to simulate the cg.gro for 1ns. i took the cg.top from the tutorial but did few modifications to suit with my structure, DPPC. however, when i added the water to the box, the water was not automatically get into the cg.top file. it is because, when i used the oplsaa force field .top file (oplsaa.top) before this, whenever you add the water, your .top file will automatically added with water coordinates. do you have any idea to why this thing happened?
your kind cooperation are much appreciated, sir.
million of thanks.
best,
syahida
do wee need to have .xtc file from our all-atom/ united atom simulation to complete the coarse graining?
it is because,in the tutorial,it gives 2 commands in coarse-graining part :
which is the first one is to produce cg.gro
-> g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
the second one is to produce fg2cg.xtc
-> g_fg2cg -pfg fg.top -pcg cg.top -c fg.xtc -n 1 -o fg2cg.xtc
what if we don't have fg,xtc from aa/ua simulation?
furthermore, i've tried to simulate the cg.gro for 1ns. i took the cg.top from the tutorial but did few modifications to suit with my structure, DPPC. however, when i added the water to the box, the water was not automatically get into the cg.top file. it is because, when i used the oplsaa force field .top file (oplsaa.top) before this, whenever you add the water, your .top file will automatically added with water coordinates. do you have any idea to why this thing happened?
your kind cooperation are much appreciated, sir.
million of thanks.
best,
syahida
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12 years 6 months ago #801
by xavier
Replied by xavier on topic cg mapping
It is not clear what you want to do here! If you do not have an atomistic why would you like to transform it into a CG representation!syahidah wrote: dear sir,
do wee need to have .xtc file from our all-atom/ united atom simulation to complete the coarse graining?
it is because,in the tutorial,it gives 2 commands in coarse-graining part :
which is the first one is to produce cg.gro
-> g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
the second one is to produce fg2cg.xtc
-> g_fg2cg -pfg fg.top -pcg cg.top -c fg.xtc -n 1 -o fg2cg.xtc
what if we don't have fg,xtc from aa/ua simulation?
Well ... you can simply add it by hand, this fine. If it does not appear by itself it might be because the program does not recognize the CG water as a proper solvent molecule.furthermore, i've tried to simulate the cg.gro for 1ns. i took the cg.top from the tutorial but did few modifications to suit with my structure, DPPC. however, when i added the water to the box, the water was not automatically get into the cg.top file. it is because, when i used the oplsaa force field .top file (oplsaa.top) before this, whenever you add the water, your .top file will automatically added with water coordinates. do you have any idea to why this thing happened?
your kind cooperation are much appreciated, sir.
million of thanks.
best,
syahida
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11 years 6 months ago #1183
by syahidah
Replied by syahidah on topic cg mapping
Dear Sir,
after coarse-graining few structures (mapping,topology preparation,energy minimization), i am still wondering how can we make sure that our coarse-grained structure is correct or not?
FYI, i coarse-grained my own structures by using the structures that are already coarse-grained in martini.itp file..
Your reply is greatlyappreciated.
Thank you so much
cheers,
syahida
after coarse-graining few structures (mapping,topology preparation,energy minimization), i am still wondering how can we make sure that our coarse-grained structure is correct or not?
FYI, i coarse-grained my own structures by using the structures that are already coarse-grained in martini.itp file..
Your reply is greatlyappreciated.
Thank you so much
cheers,
syahida
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