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Want to know how to create 3water:1cgwater beads
- maruthi
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11 years 10 months ago #982
by maruthi
Want to know how to create 3water:1cgwater beads was created by maruthi
Hi all,
As a i am going through tutorial, there is one file named water-1bar-303K.gro file used solvate protein, actually this file contains 1 bead for one water molecule . I want to know how this file can be generated, is it by means of any script available or option in martini. Please suggest me a solution for this, any help is greatly appreciated.
Thanks in advance
As a i am going through tutorial, there is one file named water-1bar-303K.gro file used solvate protein, actually this file contains 1 bead for one water molecule . I want to know how this file can be generated, is it by means of any script available or option in martini. Please suggest me a solution for this, any help is greatly appreciated.
Thanks in advance
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11 years 10 months ago #983
by djurre
Replied by djurre on topic Want to know how to create 3water:1cgwater beads
The file water-1bar-303K.gro contains normal Martini water: 1 bead for 4 water molecules. 3:1 and 1:1 mapping does not exist for Martini water.
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- maruthi
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11 years 10 months ago #985
by maruthi
Replied by maruthi on topic Want to know how to create 3water:1cgwater beads
Hello sir,
First of all let me thank you for a reply , but i want to know how to generate beads (4 water molecules : 1 bead). Is there any script to generate it, i want to generate water beads and solvate my protein using it. Can you please suggest me how to generate water beads.
Thanks ®ards,
Mohan
First of all let me thank you for a reply , but i want to know how to generate beads (4 water molecules : 1 bead). Is there any script to generate it, i want to generate water beads and solvate my protein using it. Can you please suggest me how to generate water beads.
Thanks ®ards,
Mohan
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11 years 10 months ago #986
by djurre
Replied by djurre on topic Want to know how to create 3water:1cgwater beads
I'm not sure if I understand your question. You want to generate a file like "water-1bar-303K.gro" containing just water beads? Why not use the existing file then? You can also use the existing file (water-1bar-303K.gro) to get a bigger or smaller system of water, using genbox (genbox -cs water-1bar-303K.gro -box 20 20 20 -o big_water_box.gro).
If this doesn't help you, you should explain more clearly WHY you want to make a new box/file.
If this doesn't help you, you should explain more clearly WHY you want to make a new box/file.
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11 years 10 months ago #987
by maruthi
Replied by maruthi on topic Want to know how to create 3water:1cgwater beads
Hi ,
Sorry for not being clear , if i want to combine 4 water molecules as one bead ,did i need to write any script ? i dont want to use the above mentioned option,i want to generate water beads myself(by writing or using already written script) , how can i do that? Is there any script mentioned in martini. Can you suggest me a direction , on what factors does we take in to account for combining four water molecules to one bead.
Thank you,
Mohan
Sorry for not being clear , if i want to combine 4 water molecules as one bead ,did i need to write any script ? i dont want to use the above mentioned option,i want to generate water beads myself(by writing or using already written script) , how can i do that? Is there any script mentioned in martini. Can you suggest me a direction , on what factors does we take in to account for combining four water molecules to one bead.
Thank you,
Mohan
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11 years 10 months ago #988
by djurre
Replied by djurre on topic Want to know how to create 3water:1cgwater beads
I still don't understand what you want. If you you want to convert an atomistic water box to an Martini water box (eg bundling the waters), we don't really have a script for that. You could however read the following paper: "The CUMULUS Coarse Graining Method: Transferable Potentials for Water and Solutes", Van Hoof et al., 2011.
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