Re: [gmx-users] g-dist

Hi Mohsen, I think you'll have to get a bit creative with g_traj to get the COMs, followed by either some simple scripting or nifty usage of paste and awk (something like: paste com1.xvg com2.xvg | awk '/^...@#;]/{print $2-$6, $3-$7, $4-$8}'). Hope it helps, Tsjerk On Dec 25, 2010 2:40 PM,

[gmx-users] g-dist

Dear All How can we measure the distance between COM of two molecules?of course in vector form! thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] g-dist

Dear justin please check this part of my .gro file. ... 630VAL C 6416 0.554 11.700 -0.442 630VAL O1 6417 0.522 11.605 -0.534 630VAL O2 6418 0.534 11.834 -0.454 6311 N2 1 2.686 2.399 2.151 6311 C20 2 2.613 2.375 2.230 6311 C14 3

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear justin please check this part of my .gro file. ... 630VAL C 6416 0.554 11.700 -0.442 630VAL O1 6417 0.522 11.605 -0.534 630VAL O2 6418 0.534 11.834 -0.454 6311 N2 1 2.686 2.399 2.151 6311 C20 2 2.613

[gmx-users] g-dist

Dear All I did the Enzyme/drug tutorial and generated complex.gro and complex.top files as was said. Now I want to measure the distance between center of mass of protein and drug I used g_dist but I could not. I entered these commands(of course I made an index.ndx and g-dist.tpr): I used from an

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear All I did the Enzyme/drug tutorial and generated complex.gro and complex.top files as was said. Now I want to measure the distance between center of mass of protein and drug I used g_dist but I could not. I entered these commands(of course I made an index.ndx

Re: [gmx-users] g-dist

Dear justin after using grompp without -maxwarn I faced these: NOTE 2 [file g-dist.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 2 Mb of data writing run input

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear justin after using grompp without -maxwarn I faced these: NOTE 2 [file g-dist.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 2 Mb

Re: [gmx-users] g-dist

Dear Justin WARNING 1 [file g-dist.mdp, line unknown]: Can only use nstype=Simple with pbc=no, setting nstype to Simple WARNING 2 [file complex.top, line 39718]: Bad box in file complex.gro Generated a cubic box 10.816 x 14.959 x9.086 Warning: atom name 6439 in complex.top and

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear Justin WARNING 1 [file g-dist.mdp, line unknown]: Can only use nstype=Simple with pbc=no, setting nstype to Simple WARNING 2 [file complex.top, line 39718]: Bad box in file complex.gro Generated a cubic box 10.816 x 14.959 x9.086 Warning: atom name