[gmx-users] Choosing more PMF-windows

Dear GROMACS users, I have recently completed running several PMF-windows. After viewing the histrogram file it seems that I need better sampling at some positions, but the histogram file starts at z=0. Is there any way to prevent g_wham from starting at 0, and instead show the real Z-coordinates

[gmx-users] Re: Choosing more PMF-windows

P.S. Using gromacs 4.0.7 On Sun, Jul 31, 2011 at 5:36 AM, Shay Teaching wrote: > Dear GROMACS users, > > I have recently completed running several PMF-windows. > After viewing the histrogram file it seems that I need better sampling at > some positions, but the histogram file starts at z=0. > Is

Re: [gmx-users] Choosing more PMF-windows

Shay Teaching wrote: Dear GROMACS users, I have recently completed running several PMF-windows. After viewing the histrogram file it seems that I need better sampling at some positions, but the histogram file starts at z=0. Is there any way to prevent g_wham from starting at 0, and instead sh

Re: [gmx-users] Choosing more PMF-windows

Distance of zero between COM of pull_group0 and pull_group1? On Sun, Jul 31, 2011 at 5:46 AM, Justin A. Lemkul wrote: > > > Shay Teaching wrote: > >> Dear GROMACS users, >> >> I have recently completed running several PMF-windows. >> After viewing the histrogram file it seems that I need better

Re: [gmx-users] Choosing more PMF-windows

Shay Teaching wrote: Distance of zero between COM of pull_group0 and pull_group1? Yes. The x-axis of the histogram plot indicates the distance along the reaction coordinate. -Justin On Sun, Jul 31, 2011 at 5:46 AM, Justin A. Lemkul > wrote: Shay Teaching

Re: [gmx-users] Choosing more PMF-windows

Ok thanks! On Sun, Jul 31, 2011 at 5:54 AM, Justin A. Lemkul wrote: > > > Shay Teaching wrote: > >> Distance of zero between COM of pull_group0 and pull_group1? >> >> > Yes. The x-axis of the histogram plot indicates the distance along the > reaction coordinate. > > -Justin > > On Sun, Jul 31,

[gmx-users] umbrella sampling

I've never actually reweighted with F-values. These are the values by which the component PMFs are shifted during WHAM after debiasing the umbrella potentials. Look at equations 6 and 7 in "The multicanonical weighted histogram analysis method for the free-energy landscape along structural

[gmx-users] Re: PRODRG tools

Hello, There are several ways to get the topology + force field for an arbitrary molecule: 1. "Maestro + Desmond" programs of the Schrodinger software pack can assign OPLS-AA force filed. The parameters are stored in the *.cms file. 2. "FFLD_SERVER" of the Schrodinger software: $SCHRODINGER/

Re: [gmx-users] umbrella sampling

thanks very much. I will test it. Sincerely, Qian - Original Message - From: chris.ne...@utoronto.ca Date: Sunday, July 31, 2011 8:58 am Subject: [gmx-users] umbrella sampling To: gmx-users@gromacs.org > I've never actually reweighted with F-values. These are the > values by which the

Re: [gmx-users] OPLSAA parameters

Thanks Justin for your guidance. By following your tips, I have now all the parameters I need... Please let me know if I am missing any [ angletypes ] or [ dihedraltypes ] for a hydrocarbon molecule. Best, [ bondtypes ] ; i j func b0 kb CTCT 10.15290 224262.4

Re: Re: [gmx-users] OPLSAA parameters

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Thursday, August 4, 2011. For all questions about CloudBroker and the CloudBroker Platfo

Re: [gmx-users] OPLSAA parameters

Elisabeth wrote: Thanks Justin for your guidance. By following your tips, I have now all the parameters I need... Please let me know if I am missing any [ angletypes ] or [ dihedraltypes ] for a hydrocarbon molecule. Seems fine to me; grompp will complain if something is missing. Is there

[gmx-users] protein ligand

Hi, I know this is off topic. Can someone please suggest independent scoring functions that can calculate binding energies between protein and ligand? Thanks and Regards, Ragothaman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sear

Re: [gmx-users] OPLSAA parameters

Hi Justin, So far I have been #including ffoplsaa.itp and running simulations. The reason I was after parameters is just to have a better indea on the FF parameters rather than just using them blindly, that's it :) Thank you, On 31 July 2011 20:03, Justin A. Lemkul wrote: > > > Elisabeth wrote

Re: [gmx-users] protein ligand

On 1/08/2011 10:19 AM, Ragothaman Yennamalli wrote: Hi, I know this is off topic. Can someone please suggest independent scoring functions that can calculate binding energies between protein and ligand? Surely there's a whole literature on this to search for... Mark -- gmx-users mailing lis