RE: [gmx-users] Forces in source code

Hi, Note that it is impossible to decompose a free energy (difference), which a PMF is, uniquely into different energy or force components. A free energy is not simply the sum of energy terms, but is the result of how different energy terms together affect the accessible phase space. The effect

Re: [gmx-users] Forces in source code

Thank You! I'll try to get what you writed, so, perhaps, I'll write about my success or its lack! 12 декабря 2010 г. 4:42 пользователь Mark Abraham написал: > > > On 12/12/10, Петр Попов wrote: > > Hello, dear gmx-users. > > I want to decompose PMF, but I can't use -rerun option for this > becau

Re: [gmx-users] RMSF or RMSD per residues

shiva birgani wrote: Dear all I want to analyze the mobility of residues in various conditions. I need to know examining the RMSF is more useful or RMSD per residue? That depends on your definition of "mobility." If you want to determine fluctuations/flexibility, then RMSF will have meanin

[gmx-users] RMSF or RMSD per residues

Dear all I want to analyze the mobility of residues in various conditions. I need to know examining the RMSF is more useful or RMSD per residue? Thanks in advance Shiva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

Re: [gmx-users] Extreme

Hi Pawan, I can add two things. First of all, the score is simply the projection of a point (conformation) onto the eigenvector. Second, extreme scores/projections, be it positive or negative, are usually most unlikely, thus corresponding to highest energy. For the lowest energies, you'd be looki

Re: [gmx-users] g_energy: Energy names magic number mismatch

Mikhail Stukan wrote: Dear Justin and Berk, Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version doesn't solve the problem, diagnostic is still the same: == Program g_energy_d, VERSION 4.5.3 Source code file: ../../../src/gmxlib/enxio.c, line:

[gmx-users] Extreme

Dear tsjerk, I am very sorry to say that your suggestions does not help but increase confusions only. I am highly obliged if you give me clear statements about the scores to understand this concept in depth. I have searched research article about this concept but failed to find even an single arti

RE: Re: [gmx-users] g_energy: Energy names magic number mismatch

Dear Justin and Berk, Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version doesn't solve the problem, diagnostic is still the same: == Program g_energy_d, VERSION 4.5.3 Source code file: ../../../src/gmxlib/enxio.c, line: 422 Fatal error: Ener

RE: [gmx-users] Invalid atom number 101717 in indexfile

Thanks for spotting that! I'd thought the system was complete when I'd done the index file - had completely forgot that I'd then gone onto generating ions! Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justi

Re: [gmx-users] Binary lennard jones

On 12/12/2010 6:25 PM, leila separdar wrote: yes I have read them many times OK, so you know how to understand how your .top files are describing the nonbonded interactions between your atom types. Now you just need to combine the two. Probably you want one atomtypes section, etc. If you wan

Re: [gmx-users] Setting up e-mail notifications

Hi, All clusters that I have used have such functionality in their queing system. Check the FAQ or ask the sysadmins. Erik boaz kan-tor skrev 2010-12-12 09.56: Hello Is there a way to set up e-mail notifications so that i can get an e-mail when a run is done? or when it stopped for some rea

[gmx-users] Setting up e-mail notifications

Hello Is there a way to set up e-mail notifications so that i can get an e-mail when a run is done? or when it stopped for some reason? -- Boaz Kan-Tor "I am a humanist, which means, in part, that I have tried to behave decently without expectations of rewards or punishments after I am dead." --