RE: [gmx-users] problem of pr.mdp file

Hi David and gmx-users, Do you have some experience on BD using Gromacs. I found the temperature set-up in the input must be somewhere of half of the target temperature (at least the output file showed like that). Other things seem normal. Could you tell me more about this? Thanks for your time.

Re: [gmx-users] LINCS

Stephen M. Dutz wrote: Hi all, Will someone please explain to me why I am seeing the following... I am running a protein/ lipid system with position restraints on the protein. I run two identical runs except in one I have lincs-iter = 1 and the other I have lincs-iter = 4. With lincs-iter

[gmx-users] LINCS

Hi all, Will someone please explain to me why I am seeing the following... I am running a protein/ lipid system with position restraints on the protein. I run two identical runs except in one I have lincs-iter = 1 and the other I have lincs-iter = 4. With lincs-iter = 1 I observe 26.0 hrs/ns

Re: [gmx-users] problem of pr.mdp file

sudheer wrote: hi gmx users i have one doubt regarding pr.mdp file of protein.(my protein doesnt contain any missing residues) This protein i have taken after run it in amber. The steps i have done are 1) pdb2gmx conversion 2) Energy minimisation in vaccum Now my doubt is whats the next step

Re: [gmx-users] problem of pr.mdp file

sudheer wrote: hi gmx users i have one doubt regarding pr.mdp file of protein.(my protein doesnt contain any missing residues) This protein i have taken after run it in amber. The steps i have done are 1) pdb2gmx conversion 2) Energy minimisation in vaccum Now my doubt is whats the next step

[gmx-users] problem of pr.mdp file

hi gmx users i have one doubt regarding pr.mdp file of protein.(my protein doesnt contain any missing residues) This protein i have taken after run it in amber. The steps i have done are 1) pdb2gmx conversion 2) Energy minimisation in vaccum Now my doubt is whats the next step ? directly i will

Re: [gmx-users] problem in bilayer simulation

pragya chohan wrote: I understood that it is a periodic boundry condition problem and used trjconv. But it writes a trajectory file. How do I make a gro file to input it into next run Thanks I guess I was wrong. trjconv does write gro files. In any case, working out how to do the restart is

Re: [gmx-users] RMSD calculations by g_rms

Hi Monika, Xavier, You can't really judge a run from the rmsd ;) g_rms and VMD should the exact same result. You might check the reference > frame you use and make sure you fit your protein using the same set of > atoms. > I concur, and Xavier, you hit the spot with referring to the reference fr