Re: [gmx-users] rerun trajectory does not match input file

2010-05-22 Thread John Shultz
Thanks Justin! On Sat, May 22, 2010 at 10:12 AM, Justin A. Lemkul wrote: > > > John Shultz wrote: >> >> Why do I get this message saying the group is empty? >> >> >> >> Analysing residue names: >> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat >> There are: 11350      OT

Re: [gmx-users] rerun trajectory does not match input file

2010-05-22 Thread Justin A. Lemkul
John Shultz wrote: Why do I get this message saying the group is empty? Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244PROTEIN residues There are: 0DNA residues Analysing P

Re: [gmx-users] rerun trajectory does not match input file

2010-05-22 Thread John Shultz
Why do I get this message saying the group is empty? Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Oth

Re: [gmx-users] rerun trajectory does not match input file

2010-05-22 Thread Justin A. Lemkul
John Shultz wrote: Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Yep, that's the purpose of make_ndx. -Justin Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul wrot

Re: [gmx-users] rerun trajectory does not match input file

2010-05-22 Thread John Shultz
Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul wrote: > > > John Shultz wrote: >> >> Thank you Justin, is there a way I can

Re: [gmx-users] rerun trajectory does not match input file

2010-05-13 Thread Justin A. Lemkul
John Shultz wrote: Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me You need to make a custom group that merges these two. -Justin Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100

Re: [gmx-users] rerun trajectory does not match input file

2010-05-13 Thread John Shultz
Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 5 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/am

Re: [gmx-users] rerun trajectory does not match input file

2010-05-13 Thread Justin A. Lemkul
John Shultz wrote: I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these fi

[gmx-users] rerun trajectory does not match input file

2010-05-13 Thread John Shultz
I am trying to rerun a simulation using this command mdrun -rerun -v -deffnm md I think I must have made a mistake when I prepared the original mdp file because I get this message Number of atoms in trajectory (3883) does not match the run input file (37770) I have these files in my directory Com