Re: [gmx-users] structure alignement :g_rmsdist

Hi, THanks for your answers. Just for be sure, with g_rmsdit the reference structure correspond to the frame at time 0?? Because in the manual the rmsd equation show that reference structure correspond to the time t=0 but the help doesn't confirm. THanks a lot for your help, 2013/6/2 Tsjerk

Re: [gmx-users] structure alignement :g_rmsdist

Hi Nawel, The reference distances are computed from the reference structure provided with the option -s. Cheers, Tsjerk On Mon, Jun 3, 2013 at 12:39 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. Just for be sure, with g_rmsdit the reference structure correspond

Re: [gmx-users] structure alignement :g_rmsdist

Thanks, the tpr file using by -s option contains the starting structure of the simulation so the reference structure correspond to the first structure. Thanks a lot , 2013/6/3 Tsjerk Wassenaar tsje...@gmail.com Hi Nawel, The reference distances are computed from the reference structure

[gmx-users] structure alignement :g_rmsdist

Hello everyone. During the calculation of the rms with g_rmsdist command , the reference and the current structure are aligned before calculating?? Regards, -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- gmx-users mailing list

Re: [gmx-users] structure alignement :g_rmsdist

See g_rmsdist -h Mark On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele nawel.m...@gmail.com wrote: Hello everyone. During the calculation of the rms with g_rmsdist command , the reference and the current structure are aligned before calculating?? Regards, -- *Mlle* Mele Nawel Master 2 In

Re: [gmx-users] structure alignement :g_rmsdist

Hi, THanks for your answers. I already seen the help for this command but when its write g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that* no fit is needed* like in standard RMS deviation as computed by g_rms what mean excatly no fit is needed??

Re: [gmx-users] structure alignement :g_rmsdist

Hi Nawel, g_rmsdist calculates the RMSD of distances, and distances are invariant to translation and rotation. Cheers, Tsjerk On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele nawel.m...@gmail.com wrote: Hi, THanks for your answers. I already seen the help for this command but when its write