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regarding Toulene ( Parametrizing a new molecule )
- Anurag
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9 years 1 month ago #4501
by Anurag
regarding Toulene ( Parametrizing a new molecule ) was created by Anurag
Dear Sir
I am working on molecular dynamics and I am learning the coarse-grained models. I am following the tutorial
"Parametrizing a new molecule" from your website .
I am stuck in the 5th step ( creating a .itp file). and unable to understand the further steps ( step: 6 Create CG simulation).
can you send me the .itp file created for toulene and explain me what to do in following steps. how to extract one frame from the mapped trajectories ??
looking forward for your help.
thankyou
I am working on molecular dynamics and I am learning the coarse-grained models. I am following the tutorial
"Parametrizing a new molecule" from your website .
I am stuck in the 5th step ( creating a .itp file). and unable to understand the further steps ( step: 6 Create CG simulation).
can you send me the .itp file created for toulene and explain me what to do in following steps. how to extract one frame from the mapped trajectories ??
looking forward for your help.
thankyou
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- helgi
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8 years 11 months ago #4534
by helgi
Replied by helgi on topic regarding Toulene ( Parametrizing a new molecule )
Hello, hello,
Parameterizing a new molecule can be quite tricky and depending on the molecule in question, therefore, the tutorial is just a general outline. If you want to learn to make Martini topology I would recombined one of our workshops – like the one this coming August.
If it helps a toluene.itp would look something like this:
[ moleculetype ]
; molname nrexcl
TOL 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 C4 1 TOL RI1 1 0
2 SC4 1 TOL RI2 2 0
3 SC4 1 TOL RI3 3 0
[constraints]
; i j funct length
1 2 1 0.248
2 3 1 0.191
3 1 1 0.248
And you can extract one fame from you mapped AA to CG trajectory (to use as initial coordinates for the CG simulation) e.g. using g_traj with –nxt as a .gro file and the –b –e selected so that only one frame is outputted.
Hope this helps,
Cheers,
- Helgi
Parameterizing a new molecule can be quite tricky and depending on the molecule in question, therefore, the tutorial is just a general outline. If you want to learn to make Martini topology I would recombined one of our workshops – like the one this coming August.
If it helps a toluene.itp would look something like this:
[ moleculetype ]
; molname nrexcl
TOL 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 C4 1 TOL RI1 1 0
2 SC4 1 TOL RI2 2 0
3 SC4 1 TOL RI3 3 0
[constraints]
; i j funct length
1 2 1 0.248
2 3 1 0.191
3 1 1 0.248
And you can extract one fame from you mapped AA to CG trajectory (to use as initial coordinates for the CG simulation) e.g. using g_traj with –nxt as a .gro file and the –b –e selected so that only one frame is outputted.
Hope this helps,
Cheers,
- Helgi
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