Re: [gmx-users] on non-equilibrium MD

Thanks Justin. Based on your answer, here I would like to ask, Suppose there is a PDB for a protein-ligand, and it is already known ligand would lead extremely significant conformation change of that specific protein. Based on the protein-ligand PDB, I would like to investigate the

Re: [gmx-users] on non-equilibrium MD

On 4/1/16 10:15 PM, Brett wrote: Dear All, For non-equilibrium MD, does it mean there would be no need for the energy minimization step, NVT equilibrium step and NPT equilibrium step before the production MD? In which situation we use non-equilibrium MD, and in which situation we use the

[gmx-users] on non-equilibrium MD

Dear All, For non-equilibrium MD, does it mean there would be no need for the energy minimization step, NVT equilibrium step and NPT equilibrium step before the production MD? In which situation we use non-equilibrium MD, and in which situation we use the production MD with energy minimization

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

Dear developers: Is it possible with only a small amount of work to modify calc_delta() in src/programs/mdrun/repl_ex.cpp to add another case to re->type such that the program sends the coordinates to the alternate .tpr information and evaluates the energy completely? This would allow for

[gmx-users] correction to a typo in the electric conversion factor in one place in the manual

Dear Mark: The value of f listed under eq. 4.11 is wrong in the gmx 5.1.2 manual. The correct value is reported on the bottom of page 7 at the start of section 2.2 on "MD Units". I verified this using the values in src/gromac/math/units.h. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] gromacs 5.1.2 and a possible bug related to energy minimization step

Hi, Indeed, this kind of glitch is intrinsic to writing a cluster of separate output files. Hopefully we can get energy writing into TNG files and now there can be enough metadata that users can have a smoother experience. Mark On Fri, 1 Apr 2016 14:21 Justin Lemkul wrote: >

Re: [gmx-users] gromacs 5.1.2 and a possible bug related to energy minimization step

On 4/1/16 9:01 AM, Brett wrote: Dear All, After running "gmx mdrun -v -deffnm em &", I run "gmx energy -f em.edr -o potential.xvg", but xmgrace indicated that the x-axis was "Time (ps)", although I think the value indicated by x-axis should be "step". Is it a bug? Not exactly what I

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

On 4/1/16 4:31 AM, bio hpc wrote: Did anybody of you wrote such script or can that be found in some repository? The specifics depend on the input file itself, and different programs write different names (an unfortunate truth that not everyone sticks to IUPAC/IUPAB nomenclature), and

[gmx-users] gromacs 5.1.2 and a possible bug related to energy minimization step

Dear All, After running "gmx mdrun -v -deffnm em &", I run "gmx energy -f em.edr -o potential.xvg", but xmgrace indicated that the x-axis was "Time (ps)", although I think the value indicated by x-axis should be "step". Is it a bug? Brett -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Error: Lost Particles while sorting

True, but last time I submitted a software request, the admins told me to wait until there was downtime. -Mick From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Szilárd Páll

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Did anybody of you wrote such script or can that be found in some repository? > El 31/3/2016, a las 13:04, Justin Lemkul escribió: > > > > On 3/31/16 6:55 AM, bio hpc wrote: >> Thanks. >> Apart from this, is is there some script that keeps my original hydrogens >> from

Re: [gmx-users] virtual site - algorithmic reasons

okay thank you very much. I will try. - samith On Thu, Mar 31, 2016 at 4:37 PM, Justin Lemkul wrote: > > > On 3/31/16 6:06 AM, Samith Rathnayake wrote: > >> Hi everyone, >> >> Recently i was used to started Bevan Lab tutorial and gone through >> specially with virtual site