[gmx-users] Range Checking error

Gaurav Chopra wrote: / Hi // // I am doing a steepest descent for the initial mdrun for a peptide and it // gives me the following error. Please advice. // // Thanks // Gaurav // --- // Program mdrun, VERSION 3.3 // Source code file:

[gmx-users] How 2 remove these warnings

Hi, I am getting these two warnings while doing the pdb2gmx steps.Please give some suggestions on this problem. WARNING 1 [file AFA.top, line 350]: No default Ryckaert-Bell. types, using zeroes WARNING 2 [file AFA.top, line 455]: No default Ryckaert-Bell. types, using zeroes Excluding 3

Re: [gmx-users] How 2 remove these warnings

Check the line as specified in the warning. And translate the atom number to its atom type. Check such combination in the [dihedral] section in the ffX-nb.itp whether there is such combination. I suspect that there is some mis-naming by pdb2gmx. Check the total charge of the molecule as

[gmx-users] LINCS Warning using mdrun

Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms

[gmx-users] Range Checking Error

// // Range checking error: // Explanation: During neighborsearching, we assign each particle to a grid // based on its coordinates. If your system contains collisions or parameter // errors that give particles very high velocities you might end up with some // coordinates being

[gmx-users] Range Checking Error

/ // // // Range checking error: // // Explanation: During neighborsearching, we assign each particle to a grid // // based on its coordinates. If your system contains collisions or parameter // // errors that give particles very high velocities you might end up with some // // coordinates

Re: [gmx-users] Range Checking Error

Gaurav Chopra wrote: Gaurav Chopra wrote: / Hi // // I am doing a steepest descent for the initial mdrun for a peptide and it // gives me the following error. Please advice. // // Thanks // Gaurav // --- // Program mdrun, VERSION 3.3 //

Re: [gmx-users] LINCS Warning using mdrun

Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max

Re: [gmx-users] LINCS Warning using mdrun

Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. How did you energy minimze your structure? What was the output of mdrun during energy

[gmx-users] Re: LINCS Warning using mdrun

/ Hi // // I get the following error when using mdrun for a protein in solution. // I have checked the structure and everything looks fine to me. Could // you suggested anything else I could do. / How did you energy minimze your structure? What was the output of mdrun during energy

Re: [gmx-users] xtc files

Thanks David, That works! On Tue, 14 Mar 2006 08:49:43 +0100, David van der Spoel wrote: YOLANDA SMALL wrote: Hi All, How do I convert xtc files exported for a subset of atoms in my system to pdb files? When I run trjconv, I get the following error message: Fatal error:

Re: [gmx-users] Re: LINCS Warning using mdrun

Gaurav Chopra wrote: / Hi // // I get the following error when using mdrun for a protein in solution. // I have checked the structure and everything looks fine to me. Could // you suggested anything else I could do. / How did you energy minimze your structure? What was the output of mdrun

Re: [gmx-users] pull.pdo AFM force

Hi all I have a short question. Could you please tell me what do the columns in pull.pdo (output file from AFM) stand for. Is there a simple way to obtain forces from AFM pulling? Thank you for help. Michal As an example, with one pulling group, and pulling in 3D, the output columns