Re: [gmx-users] structure factor

2013-01-28 Thread Alexey Shvetsov
Hello, В письме от 28 января 2013 16:06:20 пользователь Juliette N. написал: > Dear all, > > I am trying to calculate structure factor or scattering density of a > polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq -n > index > g_rdf can calculate SAXS structurefactor g_sans

[gmx-users] structure factor

2013-01-28 Thread Juliette N.
Dear all, I am trying to calculate structure factor or scattering density of a polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq -n index I provide an index file with System, Polymer (atom numbers of all polymers) and Solvent (all solvent molecules) groups. -startq rea

[gmx-users] Structure factor reference

2012-08-30 Thread Tetsuo Shu
Dear gmx users. I asked question about structure factor but I got no reply. I think it's too basic question, Then instead, can any one inform me a good reference paper or book why structure factor must calculate for all atom and not specific types like O-O, O-C, like rdf does? Thank you!! Since

[gmx-users] structure factor

2012-08-18 Thread Tetsuo Shu
Dear gmx users. I am new for MD and am learning hard but need to ask simple question,,, I have co2 + water system. I understand RDF and it can calculate with g_rdf by choosing 2 species like o-o, c-o, etc. I also want to learn structure factor. But for structure factor can only choose 1 species,

[gmx-users] structure factor

2012-08-16 Thread Tetsuo Shu
Dear gmx users. I am new for MD and am learning hard but need to ask simple question,,, I have co2 + water system. I understand RDF and it can calculate with g_rdf by choosing 2 species like o-o, c-o, etc. It is good! I also want to learn structure factor. But for structure factor can only choos

[gmx-users] structure factor

2012-01-07 Thread Juliette N.
Dear all, I am trying to calculate structure factor or scattering density of a polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq -n index I provide an index file with System, Polymer (atoms numbers of all polymers) and Solvent (all solvent molecules) groups. -startq re

[gmx-users] structure factor using g_rdf: grid option does not work

2009-05-27 Thread Suman Chakrabarty
Hi, I was trying to get the static structure factor using the following command line: g_rdf -f -s -sq -b 15000 -e 2 -endq 0.5 The output sq.xvg came as follows: 0.0 0.0 0.0861717775.32914 0.1723317292.77243 0.2585016632.64157 0.3446615728.30566

[gmx-users] structure factor

2009-02-23 Thread Alexander Malafeev
Hello, I try to calculate structure factor for coarse-grained system with g_rdf, but I get error > Fatal error: > > Error: atom (B1) not in list (5 types checked)! It is possible to calculate structure factor for coarse-grained model with g_rdf? And how I can do it? Thanks in advance. ___

[gmx-users] structure factor

2008-12-08 Thread Alexandr Malafeev
Hi, I have problem with calculation structure facor in coarse-grained system using g_rdf -sq, when I use g_rdf I get error message "Fatal error: Error: atom (B1) not in list (5 types checked)!". Please help. Thanks in advance. ___ gmx-users mailing list

[gmx-users] structure factor

2006-03-20 Thread Yousung Jung
How is pbc handled in calculating structure factors (SF) from MD simulation in general? I wrote a small program to compute SF for a box of water given the trajectory obtained from Gromacs, but it suffers from an edge effect (hard-sphere scattering). Do people (or does Gromacs) calculate radial dis