[gmx-users] Re: Re: Fwd: missing atom

...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100705/2214acfd/attachment-0001.html -- -- gmx-users mailing

[gmx-users] pressure coupling

Hi, all, I am trying to do anisotropic coupling using Parrinello-Rahman. I want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, fluctuation is 626 bar for pressure and 11.21 K for temperature.) I run

Re: [gmx-users] pressure coupling

Shuangxing Dai wrote: Hi, all, I am trying to do anisotropic coupling using Parrinello-Rahman. I want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, fluctuation is 626 bar for pressure and 11.21 K

[gmx-users] Implicit solvent

Dear gromacs Users, I found this in the web, but I wanted to know if there exists the possibility now of using implicit solvent efficiently. Thanks, Esteban A repeating question on the mailing list whether GROMACS can perform implicit solvent simulations. The answer is, not really. Over the

Re: [gmx-users] Implicit solvent

ithu wrote: Dear gromacs Users, I found this in the web, but I wanted to know if there exists the possibility now of using implicit solvent efficiently. Implicit solvent will be supported in the upcoming release. -Justin Thanks, Esteban A repeating question on the mailing list

Re: [gmx-users] how to strip velocities out of a .gro file

Hi Chris, What about: find . -name *.gro -exec sed -i -e '$q' -e '3,$s/^\(.\{44\}.\).*$/\1/' {} \; Assuming using a format %8.3f for coordinates and a single frame in the .gro file. Otherwise things will get more complicated. Cheers, Tsjerk On Sun, Jul 4, 2010 at 12:45 AM,

Re: [gmx-users] Free Energy calculations of peptide-protein binding

Hi Ehud, we recently developed an extended amber99sb forcefield + some scripts which probably can do exactly what you want (setting up alchemical mutations for any amino acid mutation except for proline). We tested it by calculating thermostability differences for a set of 100+ mutations of an

Re: [gmx-users] pressure coupling

Thanks for the response. Yes, I know that large fluctuations will be expected. But why the average was not even correct? Also, how can I reach some state ( some pressre and temperature) and know/tell that the system is in equilibrium if the average is not correct with large fluctuation? I mean I

Re: [gmx-users] Implicit solvent

On 05/07/10 16:27, Justin A. Lemkul wrote: ithu wrote: Dear gromacs Users, I found this in the web, but I wanted to know if there exists the possibility now of using implicit solvent efficiently. Implicit solvent will be supported in the upcoming release. Since it interests me too...

Re: [gmx-users] pressure coupling

Shuangxing Dai wrote: Thanks for the response. Yes, I know that large fluctuations will be expected. But why the average was not even correct? Also, how can I reach some state ( some pressre and temperature) and know/tell that the system is in equilibrium if the average is not correct with

[gmx-users] how to strip velocities out of a .gro file

Shay: that's a better idea than I had, thanks. Tsjerk: that's likely as fast as its ever going to get. this is great. I was initially worried that it would mangle the last line of the .gro in a triclinic box definition, but it seems to be ok. Thanks all, Chris. -- original message -- What

[gmx-users] problem in cluster determination : g_clustsize and trjconv -pbc cluster problem

Hi, I have run a simulation using gromacs 4.0.7 with 50 copies of amphiphilic surfactant ( in water) using Martini coarse-grained force-field. Mere visualization of trajectories shows that starting with 50 discrete copies, they gradually aggregate and finally two well-separated large micelles

Re: [gmx-users] Re: Re: Fwd: missing atom

/mailing_lists/users.php -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx- users/attachments/20100705/2214acfd/attachment-0001.html -- -- gmx-users mailing list gmx-users@gromacs.org http