Re: [gmx-users] How can i know if the protein swell during the MD simulation?

sovent accesible surface area? On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote: How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Well, why didn't I think of that? Maybe because flattening will also increase the SAS, or (partial) unfolding, or opening of two domains... :) Tsjerk On Tue, May 19, 2009 at 6:10 PM, Marius Retegan marius.s.rete...@gmail.com wrote: sovent accesible surface area? On Mon, May 18, 2009 at 11:09

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote: How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests

[gmx-users] How can i know if the protein swell during the MD simulation?

HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? How do you define the term swelling? This again sounds like another issue on defining your own criteria for the expected behavior and reading the