[gmx-users] radial pmf

hi everyone i'd like to calculate the pmf as a function of the radial distance between 2 groups by umbrella sampling. it looks like this is not currently possible. if anyone has a hacked version of gromacs to do it, i'd love a copy. but assuming that i have to hack the pull code myself, is there

[gmx-users] grompp problems

there's also a unix utility called 'dos2unix' to do this for you. it's included on most distributions. > > Message: 3 > Date: Wed, 4 Oct 2006 09:23:32 -0400 > From: "Moore, Jonathan (J)" <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] grompp problems > To: 'Discussion list for GROMACS users' > >

[gmx-users] Re: umbrella sampling pull.pdo output

> > is this perchance a bug or am i doing something > wrong? > sorry, i rtfm. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users maili

[gmx-users] umbrella sampling pull.pdo output

hi everyone i'm trying to calculate the free energy of binding of a guest and host in solution by umbrella sampling. my pull groups consist of individual atoms on the host and guest. i tried a force constant of 1/100*single bond strength. when the umbrella distance between the host and guest ato

[gmx-users] wham question

hi all does anyone have an example/tutorial of how to do umbrella sampling using gromacs & wham? i'm about to try to calculate free energies of binding using this method. i can find no information whatsoever about 'wham.gct', which is an optional input mentioned in the mdrun online reference pag

[gmx-users] lincs problems in solvated system

hi gmxers i'm able to run simulations of my molecule in vacuum for a long period of time (>1ns). the same is true for simulations of my solvent. however, when i solvate the molecule using genbox and then attempt an md run (either npt or nvt) after a successful energy minimization, i start to get l

[gmx-users] question on thermodynamic integration

hi everyone, i'd like to know whether people have attempted to do thermodynamic integration by continuously changing a constraint distance with time. i've not seen such an approach discussed on this mailing list, and i'm wondering whether it's an incredibly stupid idea for some reason i have yet t

[gmx-users] g_rdf & graph edges

hi all i encounter a "Fatal error: More than 4 graph edges per atom" when using g_rdf on a trajectory that was generated using 'pbc=full'. berk hess correctly stated that pbc=full circumvents this problem in mdrun, but i've not seen any news of this behaviour with the analysis programs. has an

[gmx-users] Re: graph edges problem

oops, i just saw berk hess's message that using pbc=full will circumvent this problem. however, pbc=full is incompatible with shake, right? and my solvent has coupled angle constraints which stuff up lincs. any other way around the problem? cheers mo __

[gmx-users] Mix solvent

karim trust is good. one possible method to generate your initial configuration is to do monte carlo insertions of solvent molecules until the desired numbers of each are present in your box. this method has the advantage that the box will be truly mixed. there are probably many codes out there