Re: [gmx-users] Which .tpr file to use for g_rms?

Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump So which .tpr file shoul

Re: [gmx-users] Which .tpr file to use for g_rms?

On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure

Re: [gmx-users] Which .tpr file to use for g_rms?

Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do th

Re: [gmx-users] writing the means of every 100 potential energies into an output file

mustafa bilsel wrote: Hi, I want to write the means of every 100 potential energies into an output file. Is there an option in Gromacs to do this? No, but it should be a trivial exercise to take a data file (i.e., .xvg) that contains this information and post-process it with the programmi

[gmx-users] writing the means of every 100 potential energies into an output file

Hi, I want to write the means of every 100 potential energies into an output file. Is there an option in Gromacs to do this? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Supp

RE: [gmx-users] Protein jumping out of water box

Yes, everyone knows why this happens. This question has been asked so often that there is a FAQ on the Gromacs web-site: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Best wishes Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-us

Re: [gmx-users] sasa calculation with different gromacs versions

Rocco Caliandro wrote: Hi everybody, I found a discrepancy in the sasa calculation between gromacs versions 4.0.2 and 4.5.1. For a trajectory generated by gmx 4.0.2. with AMBER force fiels, I calculated the sasa values by using the g_sas module taken from gromacs 4.0.2 (a) and gromacs 4.5

[gmx-users] sasa calculation with different gromacs versions

Hi everybody, I found a discrepancy in the sasa calculation between gromacs versions 4.0.2 and 4.5.1. For a trajectory generated by gmx 4.0.2. with AMBER force fiels, I calculated the sasa values by using the g_sas module taken from gromacs 4.0.2 (a) and gromacs 4.5.1 (b). I list the results

Re: [gmx-users] Which .tpr file to use for g_rms?

Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relativ

[gmx-users] Re:Re: tpbconv -zeroq results all coulombic energies to zero

Dear David: Thanks a lot for your reply. You are absolutely right! All the charges in the tpr file is zero now. This does not make much sense to me though, as the group I selected with "tpbconv" does not include all the atoms. I also tried to use other groups such as POPC or Protein and n

Re: [gmx-users] Which .tpr file to use for g_rms?

Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? like when I an using trjconv to dump my last frame (with "-pbc nojump"), which .tpr file should I use to get the exact p

Re: [gmx-users] pdb2gmx and atomtype.atp

Please file a bugzilla, uploading all of the input files needed to reproduce the problem. It appears that you can cause LP2 to be assigned an LP type if it is the first line in atomtypes.atp, but the mass and charge are still nonsense. Certainly you can manually modify the topology to fix thi

Re: [gmx-users] pdb2gmx and atomtype.atp

Gromacs version used was 4.5.3. I have added the new atomtype LP in the atomtype.atp and I have also defined the nonbonded+bonded interactions for LP. Parameters for LP were obtained from *Dixon.et.al J.Comp.Chem, 18, 1632-1646* *atomtypes.atp entry---* LP 3.0

Re: [gmx-users] pdb2gmx and atomtype.atp

Sarath Chandra wrote: Dear Gromacs users, I have a nitroxide radical with lone pairs on oxygen which has to be attached to Adenine of a RNA. I have the forcefiled for the nitroxide radical and as well as i have obtained the charges for the link atoms using resp. I use specbond.dat to make

[gmx-users] pdb2gmx and atomtype.atp

Dear Gromacs users, I have a nitroxide radical with lone pairs on oxygen which has to be attached to Adenine of a RNA. I have the forcefiled for the nitroxide radical and as well as i have obtained the charges for the link atoms using resp. I use specbond.dat to make the link between the nucleoti

Re: [gmx-users] Which .tpr file to use for g_rms?

Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will b

[gmx-users] Which .tpr file to use for g_rms?

Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the en

Re: [gmx-users] creat .gro; select force field

gromacs wrote: Hi users: I run pure water MD. I need to run different water models. How can i get spce.gro, which means how can i get .gro of spce water? How can i get .gro of TIP4P? The answer to both of these questions can be found here: http://www.gromacs.org/Documentation/How-tos/

Re: [gmx-users] Protein jumping out of water box

גדעון לפידות wrote: Hi all, I have been running nano second long simulations using Gromacs 4.0.7 and connecting them to create a long time period. on the last run the protein "jumped" out of the water box (the output files were viewed using VMD) does anyone know why this could have happened?

[gmx-users] Protein jumping out of water box

Hi all, I have been running nano second long simulations using Gromacs 4.0.7 and connecting them to create a long time period. on the last run the protein "jumped" out of the water box (the output files were viewed using VMD) does anyone know why this could have happened? Thanks, Gideon -- gmx-use

Re: [gmx-users] Re: individual lateral diffusion coefficients

Javier is your system a pure lipid bilayer + solvent or is there anything else (protein, peptides, etc)? Cheers Ángel. On Fri, 2010-12-03 at 00:42 +0100, Javier Cerezo wrote: > Hi. > > I think that these arguments are given for short-time diffusion (D1). > But at larger times all MSD curves

Re: [gmx-users] proton proton transfer

Hi Erik, I think also I can try proton-proton transfer with gromacs later when it will be implemented. best, Olga 2010/12/2 Erik Marklund > Olga Ivchenko skrev 2010-12-02 13.30: > > Dear gromacs users, >> >> I want to simulate proton transfer between water and another small >> molecule in grom