[gmx-users] remove center of mass motion

Dear All, I have a trajectory where the center of mass motion is not removed. In the mdrun.mdp file the option "comm-grps" was commented out: ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm

[gmx-users] error comm-grps=Protein SOL

Dear All, I have in a mdrun.mdp file following settings: ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps

Re: [gmx-users] error comm-grps=Protein SOL

Hi, >>2. If the option "comm-grps = Protein SOL" physical means (1b) what do >>I have to change in my simulation setup to avoid the warnings/ error >>"T-cm: inf" in the log files? >> >comm-grps = System (as you noted, it does not give the error!) I forgot to mention that my system contains exc

[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

Hi, to create some toy data I want to do a vacuum simulation of alanine dipeptide with Gromacs. I used charmm ("generate" command) to build the structure of alanine dipeptide. The structure in "charmm notation" is "ACE-ALA-CT3" and in "gromacs notation" is "ACE-ALA-NAC" . The charmm output is a

Re: [gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

Hi Chris, > did you try searching the archives? Yes I tried to search in archive for "No default Ryckaert-Bell. types", but I didn't find anything useful. But I didn't had the idea to search for the string combination: "ACE+NAC+oplsaa" . With the correction of topology file it worked. Thanks

[gmx-users] Vacuum Simulation of Alanine Dipeptide =>production run

Hi, to create some toy data I want to do a vacuum simulation of Alanine Dipeptide with Gromacs. For the production run script I used the gmx-user mailing list thread [1a-d], the tutorial [2] and the corresponding sample script [3]. 1a: http://www.gromacs.org/pipermail/gmx-users/2006-August/0232