[gmx-users] PBC after energy minimization

Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve this problem after the energy minimization but I don't have

Re: [gmx-users] about how to create angle.index with specific angles

Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. Now I am having issues opening the (.xpm) files generated that contain for example the gibbs energy landscape on the two first eigenvectors of the dPCA. If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o

[gmx-users] GROMACS 2020.2 patch release available

Hi GROMACS users, The official release of GROMACS 2020.2 is available! This second patch release again fixes issues found since the initial release of GROMACS 2020 and the release of 2020.1. We encourage all users of the 2020 series to update to 2020.2. Please see the link to the release

Re: [gmx-users] Invalid atomtype format (Justin Lemkul

On 4/30/20 7:10 AM, Sadaf Rani wrote: Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have

Re: [gmx-users] Invalid atomtype format (Justin Lemkul

Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:-