Re: [gmx-users] GROMACS 4.6.5 is released

Thank you Szillárd, that will indeed affect me and other users at the cluster. Best regards, João On Thu, Dec 5, 2013 at 8:08 AM, Szilárd Páll pall.szil...@gmail.com wrote: The first update on the redmine page does describe the source of the issue - although perhaps not in the most

Re: [gmx-users] Atomistic Simulation

Where do I take that file from? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013092.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] enthalpy and entropy using gromacs

Hi gmx users I want to obtain thermodynamic parameters for protein-ligand interaction. I know to obtain free energy and interaction energy by g_lie or g_bar and g_energy, respectively. Now, I want to know how to obtain enthalpy and entropy using gromacs. Which tool? Any help will highly

Re: [gmx-users] atom name - topology

I have not tried as wish to know before loosing time on making the topology. So each atom column needs letters - whats the maximum number of letters? Can I name them with same names (its one residue) as well as in pdb? Steven On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] Updating GTX670 PCIE speed from 5GT/s to 8GT/s resulted in about 10% speedup of md_run.

Just to re-iterate what Henk said, this tweak is rather safe and if it happens to cause problems, from what I've read/hear that will become obvious quite quickly. Hence, it is worth trying - especially if you have a CPU-GPU imbalance with your hardware and simulation system. I have personally

[gmx-users] segment fault when using editconf

Dear gromcas users, I have a receptor-ligand complex pdb file, and I want to use editconf to generate the receptor pdb file and the ligand pdb file. I use the following commands:editconf -f _comp0.pdb -o _receptor0.pdb -n index.ndxeditconf -f _comp0.pdb -o _ligand0.pdb -n index.ndxThe first

Re: [gmx-users] question

If you want Zn2+ ions to actually do something useful then rather than just balance the charges you might want more of them - otherwise they might just diffuse around. You could use the -conc flag with the -neutral flag. On 12/5/13 6:10 AM, Andrew Bostick wrote: Hi gmx users I am beginner

[gmx-users] hydrogen vibration leads to unphysical result

Hello fellow gromacs users, I am running a system of hydroxylated silica (Si-O-H) pore with carbon dioxide and propane. When I fix all the atoms of the solid, the gases can move freely in and out the pore. However, if I allow the hydrogen to vibrate (the way it's supposed to be), all the gases