[gmx-users] g_mindist after trjconv -fit give different results

Hi all, I have a system of protein+water+ions. I measured the minimum distance between one of the ions to the protein. Afterwards I fitted the trajectory using g_trjconv -fit rot+trans Did the same mindist again and the graphs are not always identical. Any suggestions? I use gromacs 4.0.5 wit

[gmx-users] g_mindist after trjconv -fit give different results

Hi Tsjerk, thanks for the reply. Will the MSD of the molecule also be affected by the fitting. I'm trying to calculate the relative diffusion coefficient of an ion near a protein. For this I thought to first fix the system according to the protein and then calculate the msd of the ion. I noti

Re: [gmx-users] New ion parameters and OPLS-AA

Hi Reza, -- Message: 4 Date: Tue, 15 Dec 2009 14:03:36 -0800 (PST) From: Reza Salari Subject: Re: [gmx-users] New ion parameters and OPLS-AA To: Discussion list for GROMACS users Message-ID: <858209.12986...@web35303.mail.mud.yahoo.com> Content-Type: text/plain; c

[gmx-users] Re: gmx-users Digest, Vol 50, Issue 97

Try installing development version: openmotif-devel Hi I want to use grace 5.1.9 (normally xmvgr). each time i do installation using " ./configure", it prompts motif not found . So i tried to find free softare openmotif (it can do the same work as motif). Having successfully installed openmo

[gmx-users] A fix to eigio.c ?

make_edi crashes on 3.3.3 (but not on 3.3.1). I think the problem is in eigio.c where the following lines were added after 3.3.1: eignr=NULL; eigval=NULL; eigvec=NULL; I guess it should be: *eignr=NULL; *eigval=NULL; *eigvec=NULL; Elad P. __