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CG-MD SIMULATION USING GROMACSHi
- doa.hawamdeh
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9 years 11 months ago #3848
by doa.hawamdeh
CG-MD SIMULATION USING GROMACSHi was created by doa.hawamdeh
Please, can you tell me if I can perform simulation of .itp files using gromacs? or just simulating .top files?
Thank you
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- Clement
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9 years 11 months ago #3849
by Clement
Replied by Clement on topic CG-MD SIMULATION USING GROMACSHi
I think you need to do some reading on the GROMACS philosophy... Check their website, you have comprehensive tutorials there.
.itp and .top file are topologies describing your particles (bonded parameters for lipids, proteins and/or solvent for instance) and your system (how much of each?), respectively. You include the first in the second, i.e. the description of each part of your system, parts you invoke with an occurrence later on ("I have 128 lipids of this type in my system"). The description of the non-bonded parameters (martini_v2.x.itp) is included in the .top file too. If you open these (text) files, their respective functions are quite apparent...
Try, read and see.
.itp and .top file are topologies describing your particles (bonded parameters for lipids, proteins and/or solvent for instance) and your system (how much of each?), respectively. You include the first in the second, i.e. the description of each part of your system, parts you invoke with an occurrence later on ("I have 128 lipids of this type in my system"). The description of the non-bonded parameters (martini_v2.x.itp) is included in the .top file too. If you open these (text) files, their respective functions are quite apparent...
Try, read and see.
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