[gmx-users] RE: g_angle

Hi Zuzana, what version are you running? I had the same problem. After couple of sleepless nights found in archives that there was a bug in version 3.3.2:-) When I followed the advice given there This is a known bug, recently introduced, but fixed again in CVS. You can edit the source code

Re: [gmx-users] Bad .tpr or .xtc files?

Hi Peggy, I suspect that in your .mdp file you have a line xtc-grps = Protein This means that the xtc file will only contain those atoms which gromacs reckognizes as amino acids, based on the list in the file aminoacids.dat. Your .tpr file which is used to base the index on, contains all atoms,

Re: [gmx-users] Bad .tpr or .xtc files?

Thank you for your reply, Tsjerk! I used gmxcheck, and got exactly the same number of atoms in xtc file as #proteinAtoms+#calciumAtoms+#chlorideAtom. I also checked my mdp file. It does have "xtc_grps = protein Ca Cl". In previous similar runs, I successfully wrote these atoms out. The only diff

Re: [gmx-users] Bad .tpr or .xtc files?

Hi Peggy, The key thing is that there's a mismatch between your .tpr file and your .xtc file. The first is used for the indexing and it may very well be that there's stuff in between the protein and the calcium. That way, the index number for Ca, which should be N(protein) + 1, is actually N(prote

Re: [gmx-users] Bad .tpr or .xtc files?

Thank you for the explanation! In fact, 2 Ca atoms are a part of the protein. They are in the PDB file passed to pdb2gmx. Water molecules are added after the protein atoms and the Ca atoms, as in the PDB file after genbox. So I suppose, in the .tpr file, atoms should be ordered as protein-Ca-water

[gmx-users] a problem about the residence

Hi all, I want to calculate the water number in the hydration shell around the solute, but I am not clear about the way to do it with the tools in gmx.I hope someone will gieve a hand?Thank you in advance! ___ gmx-users mailing listgmx-user

Re: [gmx-users] a problem about the residence

[EMAIL PROTECTED] wrote: Hi all, I want to calculate the water number in the hydration shell around the solute, but I am not clear about the way to do it with the tools in gmx.I hope someone will gieve a hand?Thank you in advance! g_rdf. _

[gmx-users] How can I install Gromacs on Window XP?

Hello, How can I install Gromacs on Window XP? Thanks a lot! Hero __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgm

Re: Re: [gmx-users] NVT and NVE

Hi Markus, Thanks for the reply. It worked fine. Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (u

Re: [gmx-users] How can I install Gromacs on Window XP?

Hero wrote: Hello, How can I install Gromacs on Window XP? See http://wiki.gromacs.org/index.php/Installation and links thereon. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Can GROMACS simulate the bond forming and breaking

Hi GMX users, Can GROMACS simulate the bond forming and breaking? Thanks. Best, Super ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

[gmx-users] Unit of diffusion coefficient

Dear list, Since the unit is not printed in the .xvg file generated by the module g_msd in GROMACS 3.3.2 version , I would like to know the unit of diffusion coefficient calculated. Is it in cm^2/ sec or m^2/sec? regards, jes __

Re: [gmx-users] Unit of diffusion coefficient

JMandumpal wrote: Dear list, Since the unit is not printed in the .xvg file generated by the module g_msd in GROMACS 3.3.2 version , I would like to know the unit of diffusion coefficient calculated. Is it in cm^2/ sec or m^2/sec? I'm pretty sure it is printed, but

Re: [gmx-users] Can GROMACS simulate the bond forming and breaking

Wei, Xiupeng wrote: Hi GMX users, Can GROMACS simulate the bond forming and breaking? Technically, yes. However if you need to ask that question, then it's highly likely that attempting such a simulation will require you to do a great deal of background reading and simulation practici