Hello, I have simulated amino acid (eg., glycine) with water solvent mixture in gromacs.. my question is .. 1] How can i find out the solvent orientation (angle made) ie.,angle made by water (HOH) with respect to alpha carbon of amino acid (eg., glycine)...?? 2] I have tried with gmx sorient command ..it gives me five outputs..sori, snor, sord, scum, scount. With sori (it gives from solvent orientation - cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos theta 0 to 1) , but with what respect is it giving i am not able to understand... 3] I wanted to calculate the angle formed between water (HOH) and alpha carbon of glycine. but if it consider the .gro file, i can calculate the angle for only the last frame... but i want to calculate the angle for the full frame (tpr/trr). How can i do it ...Can anybody kindly help me regarding this..
Thank you... <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> <#> On Mon, Apr 24, 2017 at 1:22 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > > I have simulated amino acid (eg., glycine) with water solvent mixture in > gromacs.. > my question is .. > 1] How can i find out the solvent orientation (angle made) ie.,angle made > by water (HOH) with respect to alpha carbon of amino acid (eg., > glycine)...?? > 2] I have tried with gmx sorient command ..it gives me five outputs..sori, > snor, sord, scum, scount. With sori (it gives from solvent orientation - > cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos > theta 0 to 1) , but with what respect is it giving i am not able to > understand...ie theta 1 and theta 2 > 3] I wanted to calculate the angle formed between water (HOH) and alpha > carbon of glycine. but if it consider the .gro file, i can calculate the > angle for only the last frame... but i want to calculate the angle for the > full frame (tpr/trr). How can i do it sir...Can u kindly help me regarding > this.. > Since i am referring one of ur research paper - [Glycine in aqueous > solution: solvation shells, interfacial water, and vibrational spectroscopy > from ab initio molecular dynamics]. and in other paper - [MONTE CARLO > SIMULATION STUDIES OF THE SOLVATION OF IONS. 2. GLYCINE ZWITTERION] they > have calculated the cos theta distribution functions...so i wanted to > calculate .. > > Thank you sir... > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > > > > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> > <#m_1046049965356203242_> > -- With Best Regards, DILIP.H.N Ph.D Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
