Re: [gmx-users] ascii Covariance matrix

Hi Russell, Check out the discussion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg09279.html Arneh > Hello all, > > I'm trying to handle covariance data using the ascii output from > g_covar. I let g_covar calculate a covariance matrix for 198 alpha carbons > of a protein, wh

[gmx-users] ascii Covariance matrix

Hello all, I'm trying to handle covariance data using the ascii output from g_covar. I let g_covar calculate a covariance matrix for 198 alpha carbons of a protein, which should give me a 594 x 594 matrix. This is probably a simple issue, but I'm confused by the ordering of the elements in the

Re: [gmx-users] thermodynamic integration

Hi, > is it possible to do thermodynamic integration in Gromacs using non-linear > scaling of the lamda paramerter? I'm not sure exactly what you mean, so first I'll answer what I think you mean, and then tell you what I think you ought to be asking. :) If you mean, "Is it possible to perform a

[gmx-users] thermodynamic integration

Hi all , is it possible to do thermodynamic integration in Gromacs using non-linear scaling of the lamda paramerter? __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

[gmx-users] NVT to NPT. Works on a single processor, does VT to NPT. Works on a single processor, does not work on 4 ????

> Hi > > I seem to be doing something wrong here, but cannot figure out what. > > - I have run a 200 ps NVT simulation for a lipid bilayer on 4 > processors using the gromacs-3.3.1 build. > > - The last frame from the NVT simulation was used in conjunction with > a newly written .mdp file to rest

Re: [gmx-users] PBC, lincs and bonds breaking

Paul Whitford wrote: I am trying to simulate my own structure based simulation using 3.3.2. I have developed the forcefield and it works fine without periodic boundary conditions. When I use pbc=xyz atoms that are connected in the [bonds] section of the topology get broken. What happens is 1

Re: [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????

himanshu khandelia wrote: Thanks for the reply. But why the difference between the 4-cpu and the 1-cpu ? Even if the algorithm is algebraically identical, if you add up 10^5 numbers in a different order and you can get a subtly different result, which amplifies in a chaotic system like MD sim

Re: [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????

Thanks for the reply. But why the difference between the 4-cpu and the 1-cpu ? On 10/27/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Hi > > > > I seem to be doing something wrong here, but cannot figure out what. > > > > - I have run a 200 ps NVT simulation for a lipid bilayer on 4 > > process