Re: [gmx-users] g_cluster warning

Thanks for the report Sabine. It would be nice if the original reporters could take the extra 5 seconds to copy-paste and report the command lines they used. There are way too many things that they or GROMACS could be doing wrong for any of us to spend time guessing what is going on. :-) Mark O

Re: [gmx-users] g_cluster warning

Hi, by looking into the code I could figure out some things. WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473 This warning comes from the -rmsmin option which is set to 0 by default and which controls the structure output. The problem with tpr/gro files is that g_cluster uses mass

Re: [gmx-users] g_cluster warning

Hi, I don't know. I don't know how to trigger it, and nobody has said how they triggered it :-) Mark On May 14, 2013 4:45 PM, "Preeti Choudhary" < preetichoudhary18111...@gmail.com> wrote: > should we worry about the warning ??? > > > On Tue, May 14, 2013 at 7:19 PM, Mark Abraham >wrote: > > >

Re: [gmx-users] g_cluster warning

should we worry about the warning ??? On Tue, May 14, 2013 at 7:19 PM, Mark Abraham wrote: > We'd need a lot more info to start to understand why .tpr vs .gro > does/should affect the result (or not)! > > Mark > On May 14, 2013 2:32 PM, "Sabine Reisser" wrote: > > > Hi, > > > > I'm having the s

Re: [gmx-users] g_cluster warning

We'd need a lot more info to start to understand why .tpr vs .gro does/should affect the result (or not)! Mark On May 14, 2013 2:32 PM, "Sabine Reisser" wrote: > Hi, > > I'm having the same warning, would also be interested in what it means. > > Additionally, I get different results if I use a t

Re: [gmx-users] g_cluster warning

Hi, I'm having the same warning, would also be interested in what it means. Additionally, I get different results if I use a tpr instead of a gro file in the -s option, using the same trajectory with -f. The results are completely different, for the gro file I get 42 while for the tpr file I

[gmx-users] g_cluster warning

hello everyone I am trying to cluster my data using g_cluster.I simulated the whole protein. I did the g_cluster analysis with only certain region of the protein which I specified using an index file.The program runs fine and gives 1 cluster.My concern is the warning it gives which states that :-

[gmx-users] g_cluster warning message

Hi, I have been trying to generate a pdb file using g_cluster with the following command: "g_cluster -s md.tpr -f md.xtc -cl" It ran O.K. but I am curious the rmsd warning message:   The RMSD ranges from 0.0481586 to 0.200779 nm Average RMSD is 0.124039 Number of structures for matrix 5001 Energy