Re: [gmx-users] updating amberff.03 files

5. Or you could just leave your solution in the same form as you did for the 4.0.x GROMACS. Mark On Thu, Apr 11, 2013 at 10:36 PM, Laura Kingsley** wrote: Hello Gromacs Users, I am trying to update the contents of the top folder. I have parameters for a HEME residue that worked in gromacs

Re: [gmx-users] updating amberff.03 files

in the .itp file generated by pdb2gmx the dihedral type for the heme is given as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not sure where its reading this from. I'm hoping that this is just a simple thing that I'm missing and someone can help point me in the

[gmx-users] updating amberff.03 files

y pdb2gmx the dihedral type for the heme is given as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not sure where its reading this from. I'm hoping that this is just a simple thing that I'm missing and someone can help point me in the right direction. Thanks, -

[gmx-users] make_ndx: duplicates groups appearing in index.ndx file

:73 atoms 28 JJJ : 1 atoms 29 CPZ :19 atoms 30 Cl : 6 atoms 31 Water_and_ions : 119316 atoms Thanks, - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: R

Re: [gmx-users] PMF trails off to infinity.

p1 = CPZ pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = pull_init1 = 0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1= On 07/02/2012 04:38 PM, Justin A. Lemkul wrote: On 7/2/12 4:30 PM, Laura Kings

Re: [gmx-users] PMF trails off to infinity.

quette -Justin -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] PMF trails off to infinity.

uld email them directly to you? Let me know. Thanks, - Laura On 07/02/2012 03:42 PM, Justin A. Lemkul wrote: On 7/2/12 9:54 AM, Laura Kingsley wrote: Hello, I am using steered MD and umbrella sampling to generate a PMF profile for pulling a small ligand 3 nm. As I pull the ligand from 3A

[gmx-users] PMF trails off to infinity.

going wrong here? I am thinking this probably isn't correct, but I don't know where I've messed up. Thanks! I can attach the graphs if necessary. - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

it uses SMD to generate the initial configurations for different windows and then perform umbrella sampling separately on each windows to subsequently extract the PMF using WHAM based on the data set on umbrella sampling. -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular

Re: [gmx-users] Jarzinsky's inequality from SMD simulation

F from SMD simulations. If not, can anyone suggest some guidelines how to do it. Sanku -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing l

Re: [gmx-users] AFM pulling simulations

simulations with gromacs? Thanks, -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Umbrella sampling windows

in advance, Susana -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

Re: [gmx-users] Umbrella sampling windows

ions where there is no overlap or to increase the force constant ? If I increase the force constant can I continue the simulation with the new constant or do I have to start again? I used a force contant of 3000 kJ mol^-1 nm^-2. Thank you in advance, Susana -- Laura Kingsley Graduate Student