normal newbies in CGMD

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8 years 1 month ago #634 by syahidah
newbies in CGMD was created by syahidah
dear all martini users,
for your information,i am doing a project which includes the coarse grain molecular dynamics simulation.
thus, i need to prepare the coarse grained structure for the structures that will be used in the simulation, such as lecithin, cremophore.
i have gone through the papers that study about the CGMD. however i can not find the detailed method for the preparation of cg model.

may i have the methods for 4 to 1 mapping?and may i know what command or program/software that you use to do the coarse graining and 4 to 1 mapping?fyi, i am so new with this, and honestly, i am still confuse on how to create input files for CG structure that are needed in order to run the simulation for CG-MD.

i've read in "GROMACS Coarse-Graining Workshop CSC, Helsinki, Finland January 28-30, 2009" tutorial paper where it has been stated that the g_fg2cg can produce the coarse grained structure .however, when i check with my GROMACS version (VERSION 4.5.3), the command was not found. is it mean that i need to install it separately? is this command applicable to lipid structure (i'm using phosphatidylcholine and cremophor for my project).

sorry for asking this sir,
would you mind to give me a complete tutorial on how to model the CG structure (lipid) and also the tutorial on how you prepare the input files for CG structure.
i do really appreciate your cooperation sir, feel free to advise me.

thank you.
best,

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8 years 1 month ago #641 by xavier
Replied by xavier on topic newbies in CGMD
Dear Syahidah,

there are a couple of tutorial that you'll find on the website, they are in the "Tutorial" section ... this is a good start to get a feeling on what CGMD is ...

have fun,
XAvier.

syahidah wrote: dear all martini users,
for your information,i am doing a project which includes the coarse grain molecular dynamics simulation.
thus, i need to prepare the coarse grained structure for the structures that will be used in the simulation, such as lecithin, cremophore.
i have gone through the papers that study about the CGMD. however i can not find the detailed method for the preparation of cg model.

may i have the methods for 4 to 1 mapping?and may i know what command or program/software that you use to do the coarse graining and 4 to 1 mapping?fyi, i am so new with this, and honestly, i am still confuse on how to create input files for CG structure that are needed in order to run the simulation for CG-MD.

i've read in "GROMACS Coarse-Graining Workshop CSC, Helsinki, Finland January 28-30, 2009" tutorial paper where it has been stated that the g_fg2cg can produce the coarse grained structure .however, when i check with my GROMACS version (VERSION 4.5.3), the command was not found. is it mean that i need to install it separately? is this command applicable to lipid structure (i'm using phosphatidylcholine and cremophor for my project).

sorry for asking this sir,
would you mind to give me a complete tutorial on how to model the CG structure (lipid) and also the tutorial on how you prepare the input files for CG structure.
i do really appreciate your cooperation sir, feel free to advise me.

thank you.
best,

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8 years 1 month ago #643 by syahidah
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yes sir,
i found few tutorial for lipids. however, i'm a little bit confuse about the .gro file. may i know how do you produce .gro file for CG structure?

because, for MD i did antechamber by using amber8 in order to get the .gro file.

thank you,
best,
syahida

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8 years 1 month ago #644 by xavier
Replied by xavier on topic newbies in CGMD
Dear Syahidah,

There is also a tutorial on proteins ...

There is no general script that generates a CG gro file from an atomistic file. The only general way to do this is by using the "reverser" transformation code of gromacs. It implies that the mapping is defined in the topology file. It is a rather advanced procedure. I would not advise you to use it before you have been through the tutorials and manage to do some CG simulations with gromacs.

There are scripts for generating the protein gro file ... look for the tutorial if you need.

Typical lipid system's topologies and gro files can be found in he "download" section of the website.

XAvier.

syahidah wrote: yes sir,
i found few tutorial for lipids. however, i'm a little bit confuse about the .gro file. may i know how do you produce .gro file for CG structure?

because, for MD i did antechamber by using amber8 in order to get the .gro file.

thank you,
best,
syahida

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8 years 1 month ago #645 by syahidah
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could i take the gro file that provided in the tutorial although my system is not bilayer. so do you mean that i can straight away take the .gro file (e.g:dspc_single.gro) and try to do CG simulation?

sir,could i use spc216.gro for water instead of water.gro? because i tried to solvate the molecule by using water.gro(provided in lipid_tutorial)but failed. so i replaced it with spc216.gro.and i got the water molecules but not in cg formation.fyi, i used GROMACS 4.5.3 and the command i used is:

to create simulation box:
editconf -f dspc_single.gro -o dspc_single-pbc.gro -bt cubic -box 7.5 -d 0.8 -c

to add solvent water:
genbox -cp dspc_single-pbc.gro -cs spc216.gro -p dspc.top -o dspc_single-wat.gro

actually, this is the command that i've used to run MD simulation

besides, i was wondering how did you get the gro files. what command/software did you use sir?

and for "reverser", i found that the one that attached in the tutorial is GROMACS version 3.3.1.am i right sir?so how about version 4.5.3?

your cooperation are much appreciated sir.=)
thank you,

best,
syahida

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8 years 1 month ago #646 by xavier
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syahidah wrote: could i take the gro file that provided in the tutorial although my system is not bilayer.

Obviously not! Think about it!

syahidah wrote: so do you mean that i can straight away take the .gro file (e.g:dspc_single.gro) and try to do CG simulation?

You could but then it would be about the system that is in the gro file.

syahidah wrote: sir,could i use spc216.gro for water instead of water.gro? because i tried to solvate the molecule by using water.gro(provided in lipid_tutorial)but failed. so i replaced it with spc216.gro.and i got the water molecules but not in cg formation.

No you should not use the spc216.gro! it contains atomistic water so it is clearly not appropriate for CG simulations! Try to fix the problem you had with water.gro. It should work.

syahidah wrote: fyi, i used GROMACS 4.5.3 and the command i used is:

to create simulation box:
editconf -f dspc_single.gro -o dspc_single-pbc.gro -bt cubic -box 7.5 -d 0.8 -c

to add solvent water:
genbox -cp dspc_single-pbc.gro -cs spc216.gro -p dspc.top -o dspc_single-wat.gro

actually, this is the command that i've used to run MD simulation

besides, i was wondering how did you get the gro files. what command/software did you use sir?

It is a combination of scripts and programs from the gromacs suite that allows generating a CG gro file.

syahidah wrote: and for "reverser", i found that the one that attached in the tutorial is GROMACS version 3.3.1.am i right sir?so how about version 4.5.3?

This is right. But again I would suggest you go through the tutorials for lipids and proteins prior using the reverse transformation. I will not help you going through it before you can actually run a CG simulation and understand what a topology is ...

syahidah wrote: your cooperation are much appreciated sir.=)
thank you,

best,
syahida

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8 years 1 month ago #647 by syahidah
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sir,
i am so sorry for asking this,
did you use vmd to visualize the graphical images?

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8 years 1 month ago #648 by xavier
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syahidah wrote: sir,
i am so sorry for asking this,
did you use vmd to visualize the graphical images?


yes.

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8 years 4 weeks ago #649 by syahidah
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sir,
i'm doing the tutorial suggested by you.
it's lipid tutorial,

however, when i want to do the secongd minimization (to adapt dspc.top to reflect water beads to the system). the system gave:

Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (waterbox.gro, 2560)
does not match topology (dspc.top, 1792)


your cooperation are much appreciated sir,
thank you,
best,
syahida

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8 years 4 weeks ago #650 by syahidah
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i checked the waterbox.gro and dspc.top files.
and the number of water and dspc is same for both file.

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8 years 4 weeks ago #651 by xavier
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syahidah wrote: sir,
i'm doing the tutorial suggested by you.
it's lipid tutorial,

however, when i want to do the secongd minimization (to adapt dspc.top to reflect water beads to the system). the system gave:

Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (waterbox.gro, 2560)
does not match topology (dspc.top, 1792)


your cooperation are much appreciated sir,
thank you,
best,
syahida


The message clearly indicates that there is a mismatch! Is it the waterbox.gro you should be giving?

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8 years 4 weeks ago #652 by syahidah
Replied by syahidah on topic newbies in CGMD
sir,
the dspc.top is:

#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"

[ system ]
DSPC BILAYER SELF-ASSEMBLY

[ molecules ]
DSPC 128
;W 768

sir,
in my humble opinion,
i think that 1792 is come from 128 coarse-grained DSPC.
for each DSPC, there are 14 interaction sites.

1DSPC NC3 1 3.005 2.281 4.585
1DSPC PO4 2 3.404 2.076 4.440
1DSPC GL1 3 3.367 1.834 4.043
1DSPC GL2 4 3.049 1.704 3.959
1DSPC C1A 5 3.554 1.492 3.805
1DSPC C2A 6 3.851 1.154 3.646
1DSPC C3A 7 3.851 0.749 3.415
1DSPC C4A 8 3.661 0.325 3.313
1DSPC C5A 9 3.238 0.152 3.323
1DSPC C1B 10 3.153 1.680 3.520
1DSPC C2B 11 3.136 1.604 3.057
1DSPC C3B 12 3.133 1.325 2.677
1DSPC C4B 13 2.896 0.930 2.507
1DSPC C5B 14 2.429 0.864 2.436
128 will give 1792.

then 2560 is the total number of DSPC interaction sites/beads + with 768 no. of water.

but i wonder why is it defined as 1792 in dspc.top file because we put the no of dspc is 128.

what should i change sir?

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8 years 4 weeks ago #653 by xavier
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syahidah wrote: sir,
the dspc.top is:

#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"

[ system ]
DSPC BILAYER SELF-ASSEMBLY

[ molecules ]
DSPC 128
;W 768

sir,
in my humble opinion,
i think that 1792 is come from 128 coarse-grained DSPC.
for each DSPC, there are 14 interaction sites.

1DSPC NC3 1 3.005 2.281 4.585
1DSPC PO4 2 3.404 2.076 4.440
1DSPC GL1 3 3.367 1.834 4.043
1DSPC GL2 4 3.049 1.704 3.959
1DSPC C1A 5 3.554 1.492 3.805
1DSPC C2A 6 3.851 1.154 3.646
1DSPC C3A 7 3.851 0.749 3.415
1DSPC C4A 8 3.661 0.325 3.313
1DSPC C5A 9 3.238 0.152 3.323
1DSPC C1B 10 3.153 1.680 3.520
1DSPC C2B 11 3.136 1.604 3.057
1DSPC C3B 12 3.133 1.325 2.677
1DSPC C4B 13 2.896 0.930 2.507
1DSPC C5B 14 2.429 0.864 2.436
128 will give 1792.

then 2560 is the total number of DSPC interaction sites/beads + with 768 no. of water.

but i wonder why is it defined as 1792 in dspc.top file because we put the no of dspc is 128.

what should i change sir?


The line relative to water is commented! A character ";" indicates that the line will not been taken into account.

XAvier.

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8 years 3 weeks ago #654 by syahidah
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sir,now i'm doing the refine CG parameters based on AA simulation.

there are choices for me to this right?

however, i can not find the transformed trajectory (fg2cg.xtc) in tarball.

thank you,
best,
syahida

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8 years 3 weeks ago #656 by xavier
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syahidah wrote: sir,now i'm doing the refine CG parameters based on AA simulation.

there are choices for me to this right?

I am not sure what you mean here!

however, i can not find the transformed trajectory (fg2cg.xtc) in tarball.

Here neither!

thank you,
best,
syahida

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8 years 3 weeks ago #658 by syahidah
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sorry sir,
i will make it clear.
actually after doing the self-assembly,i'm going to do the refine part.
the tutorial states that i can do the refine art by using g_fg2cg.
the tuturial states that g_fg2cg is in the tarball, IMO, it means that the g_fg2cg is in the refine folder in lipid tutorial. however, there is no g_fg2cg file.
do i need another step to get this g_fg2cg?

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8 years 3 weeks ago #661 by xavier
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syahidah wrote: sorry sir,
i will make it clear.
actually after doing the self-assembly,i'm going to do the refine part.
the tutorial states that i can do the refine art by using g_fg2cg.
the tuturial states that g_fg2cg is in the tarball, IMO, it means that the g_fg2cg is in the refine folder in lipid tutorial. however, there is no g_fg2cg file.
do i need another step to get this g_fg2cg?


I am not familiar with this tutorial. I guess that to use the g_fg2cg you have to install the modified version of gromacs. Did you do this?

XAvier.

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8 years 3 weeks ago #663 by syahidah
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sir,
in the tutorial, they attach rev_trans.tar.gz
after i download and extract it,
i found that it is GROMACS 3.3.1,
so i'm a bit confuse whether this is the special version for reverser or just the latest version during the workshop is hold.
FYI, now i'm using GROMACS 4.5.3,
can i just proceed with the version that i already have?
but the problem is there is no g_fg2cg.

thank you,
best,
syahida

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8 years 3 weeks ago #666 by xavier
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syahidah wrote: sir,
in the tutorial, they attach rev_trans.tar.gz
after i download and extract it,
i found that it is GROMACS 3.3.1,
so i'm a bit confuse whether this is the special version for reverser or just the latest version during the workshop is hold.

No you actually have to install the version that is gioven in the following link.

md.chem.rug.nl/cgmartini/images/stories/tutorial/gmx_rev.tar.gz

FYI, now i'm using GROMACS 4.5.3,
can i just proceed with the version that i already have?
but the problem is there is no g_fg2cg.

No the reverse transformation is not implemented in GMX4.X versions. Only the one in the

thank you,
best,
syahida

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7 years 11 months ago #683 by syahidah
Replied by syahidah on topic newbies in CGMD
hi sir,
i did tutorial for g_fg2cg
however,i'm little bit wondering on how we can get the cg.gro file for the molecules that is not included in the forcefield library.meaning that, if molecules like dupc and dspc, they are already have the topology in the martini.itp,but how about the other molecule? i'm wondering is there any steps to produce *_fg.itp to *_cg.itp?

thank you sir,
your reply much aprreciated sir.

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