Re: [gmx-users] comm_mode

[EMAIL PROTECTED] wrote: Dear users, There is an option in .mdp named comm_mode, which deals with the transition and rotation of the molecule being simulated. I want to know why the transition and rotation happens during the simulation. Can any one suggest me any reading material where in I ca

Re: [gmx-users] gromacs-3.3.1 installation problem

Chenyue Xing wrote: Hi all, I'm trying to install gromacs-3.3.1. I first installed fftw-3.0.1 with --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw include/ and lib/ directories. ./configure successfully passed all checking (seems so) but it stopped at ' config.status: executing dep

Re: 回复： Re: 回复： Re: [gmx-users ] Is 2D projection in g_anaeig

xi zhao wrote: Dear sir: I am sorry. Can I understand" 2D projection = Probability Distributions P(v1,v2) in Proteins 2005; 60:485. How to produce 3D Don't know the paper, but such a projection can give you a probability distribution if you histogram it. plot of P(v1,v2)? how can I look

[gmx-users] regarding comm_mode

Dear users, There is an option in .mdp named comm_mode, which deals with the translation and rotation of the molecule being simulated. I want to know how and why the translation and rotation happens during the simulation and their significance. Can any one suggest me any reading material where

[gmx-users] comm_mode

Dear users, There is an option in .mdp named comm_mode, which deals with the transition and rotation of the molecule being simulated. I want to know why the transition and rotation happens during the simulation. Can any one suggest me any reading material where in I can find how the dynamics is

[gmx-users] gromacs-3.3.1 installation problem

Hi all,   I'm trying to install gromacs-3.3.1. I first installed fftw-3.0.1 with --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw include/ and lib/ directories. ./configure successfully passed all checking (seems so) but it stopped at ' config.status: executing depfiles commands' and didn'

回复： Re: 回复： Re: [gmx-use rs] Is 2D projection in g_anaeig

Dear sir: I am sorry. Can  I understand" 2D projection = Probability Distributions P(v1,v2) in Proteins 2005; 60:485. How to produce 3D plot of P(v1,v2)? how can I look for transit paths from  P(v1,v2)? How can I calculate free enery in gromacs using P(v1,v2)? Thank you in advance! David van der

[gmx-users] segmentation fault

Dear GMX users, I am studying adsorption of polymers on a surface. I want to enforce all polymers to be adsorbed, so I increase 10 times of the LJ interaction between polymers and the surface, then I got segmentation fault. Without increasing, the program ran fine (some polymers are not adsorbed)

Re: 回复： Re: [gmx-users] Is 2D projec tion in g_anaeig

xi zhao wrote: Dear sir : Can I understand" 2D projection = Component (PC) Probability Distributions P(v1,v2)"? If this is a true, and how to define the Pmax in detail? Thank you in advance! you can specify the vectors you want with -v1 -v2 */Nguyen Hoang Phuong <[EMAIL PROTECTED]>/* 写道：

回复： Re: [gmx-users] Is 2D projection

Dear sir : Can I understand" 2D projection = Component (PC) Probability Distributions P(v1,v2)"? If this is a true, and how to define the Pmax in detail? Thank you in advance! Nguyen Hoang Phuong <[EMAIL PROTECTED]> 写道： > Dear gmx users,>> Does the 2D projection plot has something to do with conv