Re: [gmx-users] Bromide ions in gromos forcefield

ts.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't

[gmx-users] genbox generating acetonitrile box with holes

Dear all, I tried to send this message earlier, but I had attached a pdb file and apparently it exceeded the size allowed in the mailing list and is awinting for the list moderator to evaluate it. I apologize if the message is sent twice. I am trying to solvate a protein in a box of acetonitrile u

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

istinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.g

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

gt; reading, sorry. But are these holes created by genbox, or are they already > present in the acn solven box? Have you already checked all intermediate > structures? > > Cheers, > > Tsjerk > > On Nov 6, 2010 7:25 PM, "Diana Lousa" wrote: > > Hello, > &

[gmx-users] g_hbond and hydrogen bonds involving sulfur

Dear all, Does any know why g_hbond does not (at least in a straightforward way) enable the calculation of hbonds involving sulfur atoms (e.g. between cysteines and other residues)? Is there an easy way to tell gromacs to consider sulfur a donor and acceptor atom? Thanks in advance Diana Lousa

Re: [gmx-users] g_hbond and hydrogen bonds involving sulfur

Diana Lousa Protein Modelling Laboratory Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Portugal On Thu, 15 Oct 2009, Justin A. Lemkul wrote: Diana Lousa wrote: Dear all, Does any know why g_hbond does not (at least in a straightforward way) enable the

Re: [gmx-users] Alchemistry free energy simulations of molecules with different atom numbers

o circumvent the problems associated with growing or disappearing particles out of nothing I used soft-core interactions and manipulated the soft-core parameters to get "nice" dgdl curves. Hope this helps. Diana Lousa PhD student Protein Modelling Laboratory ITQB/UNL Oeiras, Portugal >

[gmx-users] Nomenclature Inconsistency between *.rtp and *nb.itp in ffG53a5 and ffG53a6 (CH2r vs CH2R)

1 CB CH2R 0.0 1 CG CH2R 0.0 2 CD CH2R 0.0 2 C C 0.450 3 O O -0.450 3 Is GROMACS case sensitive?. Can this be a source of errors? Thanks in advance. -- Diana Lousa PhD student Protein Modelling Laboratory ITQB

[gmx-users] Re: forward and reverse free energy not consistant (Li Qiang)

ou're referring to, I checked the reported known bugs and didn't find anything that was likely to cause this strange results. Thanks Diana Lousa Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av. da República – EAN, 2780-157 Oeiras PORTUGAL -- Fo