[gmx-users] RDF com

Hello, I am trying to calculate the rdf using the center of mass of a sulfonate group, SO3 with other SO3 groups in the system. The SO3 group is part of a bigger molecule. Is it appropriate to use gmx rdf -rdf mol_com to carry out this operation or should I use the gmx rdf -yescom In each case

[gmx-users] radial density profiles gmx

Hello, I am simulating reverse micelles and want to calculate radial density profiles of water trapped inside the RM. I looked up the gmx density, but it looks like it is geared for bilayers. I am wondering if anyone has used gmx density or some other tool to calculate radial density of speciified

Re: [gmx-users] RDF com

On 10/17/15 5:32 AM, Deva Priya wrote: Hello, I am trying to calculate the rdf using the center of mass of a sulfonate group, SO3 with other SO3 groups in the system. The SO3 group is part of a bigger molecule. Is it appropriate to use gmx rdf -rdf mol_com to carry out this operation or shou

Re: [gmx-users] RDF com

Thanks a lot, Justin. On Sat, Oct 17, 2015 at 8:02 AM, Justin Lemkul wrote: > > > On 10/17/15 5:32 AM, Deva Priya wrote: > >> Hello, >> >> I am trying to calculate the rdf using the center of mass of a sulfonate >> group, SO3 with other SO3 groups in the system. The SO3 group is part of a >> big

Re: [gmx-users] Energy minimization error

Dear gromacs users, As I said before I faced with the minimization error, so I changed coordinates of atoms in pdb file, but the problem is the same. the only thing that changes in every run is atom number. I modified pdb for many times. Steepest Descents converged to Fmax < 1000 in 530 steps Pot

[gmx-users] constraining charges

Hi All, I have some amino-acid residue in which some extra side chain(s) attached by replacing H from amino-acid. I want to simulate this with CHARMM ff. Somehow I can choose best bonded params. But in order to keep integral charge on this modified aminoacid I was thinking if there is any way to

Re: [gmx-users] Energy minimization error

Hi, What some visualization program shows about bonds doesn't mean anything - it has not parsed your topology. You have no option but to look at the .top produced and reason about what it shows, but yours is very complex. I strongly recommend starting with something simpler than a multiply branche

[gmx-users] Message-ID: Content-Type: text/plain; charset=UTF-8

Hey Mark, I tried to set the CMAKE_LIBRARY_PATH to an actual file, because it cannot be found by cmake if I left it out, but it is there. Greetings Kim > > Ursprüngliche Nachricht: > > Von: Kim Jessica Novacek > > An: gromacs.org_gmx-users@maillist.sys.kth.se > > Kopie: > > Datum: Mon Oct 12 1