normal martini 2.1 vs martini 2.2

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1 month 1 week ago #9124 by Subhadra
martini 2.1 vs martini 2.2 was created by Subhadra
Hi everyone,
I have calculated SASA (Solvent Accessible Surface Area) for peptides FF, FW and GG using Martini 2.1 and Martini 2.2. They (SASA) are not in agreement with each other for FF and FW but are in agreement for peptide GG. I am not quiet sure what led to the difference in SASA for FF and FW. Can anyone please help me to understand this?

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1 month 1 week ago #9125 by xavier
Replied by xavier on topic martini 2.1 vs martini 2.2
Hi you,

Your question Is quite confusing … from your way to ask, it is not possible to indicate the difference between any peptides of any sort …

May be you want to ask the possible difference between the Versions Martini-2.2 and 2.1? As you observe between two out of three peptides?

In that case I am personally not sure but some VdW radius used for calculating the SASA might have been modified. It depends how you calculate SASA as the software you use will define VdW radii and potentially other details …

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1 month 1 week ago #9126 by xavier
Replied by xavier on topic martini 2.1 vs martini 2.2
Hi you,

Your question Is quite confusing … from your way to ask, it is not possible to indicate the difference between any peptides of any sort …

May be you want to ask the possible difference between the Versions Martini-2.2 and 2.1? As you observe between two out of three peptides?

In that case I am personally not sure but some VdW radius used for calculating the SASA might have been modified. It depends how you calculate SASA as the software you use will define VdW radii and potentially other details …

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