[gmx-users] ParmED

be wrong? Best -- Hosein Geraili Daronkola Ph.D. student, Wissenschaftspark Potsdam-Golm Max Planck Institute of Colloids and Interfaces Theory and Bio-Systems Department Office K-1.119 Am Mühlenberg 1 OT Golm 14476 Potsdam Germany Phone: +49-(0)331 567-9611 Fax: +49-(0)331 567-9602 E-mail

[gmx-users] thermostat

? Best -- Hosein Geraili Daronkola Ph.D. student, Wissenschaftspark Potsdam-Golm Max Planck Institute of Colloids and Interfaces Theory and Bio-Systems Department Office K-1.119 Am Mühlenberg 1 OT Golm 14476 Potsdam Germany Phone: +49-(0)331 567-9611 Fax: +49-(0)331 567-9602 E-mail

[gmx-users] temperature of a group

Hi,How can I get the temperature of a certain group from .edr or .trr, like the gmx energy, but the problem with gmx energy is, it just gives the temperature for the whole system. Best -- Gromacs Users mailing list * Please search the archive at

[gmx-users] -t state.cpt

Hi all, What would happen if someone would not use -t previous_state.cpt in the production run?? Isn't that the case that gromacs can read the velocity from the last frame .gro file of the previous simulation? Best -- Gromacs Users mailing list * Please search the archive at

[gmx-users] polymer state

Dear all, How can I find the polymer state (monomer, dimer, trimer, ...?) of a protein? I thought it would be the REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT in the pdb file,but for a protein, I read in its article that it is monomer in solution, and this REMARK was HEXAMERIC!!!I need to

[gmx-users] Changing Sigma in force field

Dear all,I am trying to change the epsilon of one atom type in the Amber force field, and because I have some atom in this type that I don't want to be changed, I defined a new atom type. I mean I add in all the files in the force field.ff directory that has that atom type a new atom type with

[gmx-users] Scaling factor on Sigma and epsilon

Dear all,I need to use two separate scaling factor on O-O(self interaction epsilon) and K-O(scaling factor on the result of Lorentz-Berthelot sigma). I have several O with the same name in my force field, but I just want this effect on two of them.How can I do that without affecting other atoms

[gmx-users] .gro file

I have a .gro file in which the atoms and the box size is a rectangular cube, and I need to change it to a cube. How can I do that?Best -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] make_ndx

Dear all,I need to use make_ndx, but it doesn't work. I mean, I will put my group numbers, and it finishes successfully, but at the end there is nothing in the .ndx file.  0 System              : 24552 atoms  1 Other               :    576 atoms  2 ACC                 :   504 atoms  3 K+         

[gmx-users] Fw: .gro file shows the wrong mass

Dear all, I tried to create Potassium-acetate .gro file using "acpype", and the same procedure works well with Sodium-acetate. The problem is when I open the .gro file in VMD for NA_ACC the mass for Sodium is correct, but for K_ACC it shows the mass of Potassium as 12 which is wrong.I

[gmx-users] .gro file shows the wrong mass

Dear all, I tried to create Potassium-acetate .gro file using "acpype", and the same procedure works well with Sodium-acetate. The problem is when I open the .gro file in VMD for NA_ACC the mass for Sodium is correct, but for K_ACC it shows the mass of Potassium as 12 which is wrong.I attached

[gmx-users] umbrella sampling tutorial

Dear all, I have a question regarding the umbrella sampling tutorial. I am using the bash script to create the summary_distances.dat, but the problem is at first I would get the error "Unknown command-line option -o", then I used -oh instead of -o which worked, but the problem is the