[gmx-users] Re: gmx-users Digest, Vol 55, Issue 150

Dear Justin and all, In my results, that are not only 8 micelles but there are 2 aggregated micelles and some free monomers that made up total of 8. Then the graph also showed 8 number of clusters. that is what I am wonder is it monomer also counted? thanks for any comments. QIU YI HUAN A begin

[gmx-users] g_order post - 3.3.1 (yes, again).

Hello all, I've been having a nightmare of a time trying to get order parameters for my lipids.  All pre-3.3 files I have can be processed quite happily with a version of g_order from 3.2.1, but I can't seem to get 4.0 (or 3.3.1) to produce the basic order.xvg.  I've tried specifying all carbons

Re: [gmx-users] g_order post - 3.3.1 (yes, again).

Alan Dodd wrote: Hello all, I've been having a nightmare of a time trying to get order parameters for my lipids. All pre-3.3 files I have can be processed quite happily with a version of g_order from 3.2.1, but I can't seem to get 4.0 (or 3.3.1) to produce the basic order.xvg. I've tried spe

Re: [gmx-users] Re: gmx-users Digest, Vol 55, Issue 150

Q. Y. HUAN wrote: Dear Justin and all, In my results, that are not only 8 micelles but there are 2 aggregated micelles and some free monomers that made up total of 8. Then the graph also showed 8 number of clusters. that is what I am wonder is it monomer also counted? thanks for any comments

[gmx-users] RE: defination of cluster

Dear Justin, I didn't use any of the options. I just use this command: g_clustersize -f md1.xtc -s md1.tpr -n index.ndx -o -ow -nc -ac -mc . all with default file name. I didnt use other options. Thanks a lot. ___ gmx-users mailing list

[gmx-users] conjugate gradient with dummies

Hello, I am trying to run two step energy minimization with steep followed by cg on a structure with hydrogen vsites and heavyh (in OPLSAA). In gromacs 3.3.3 I had an error in grompp when starting cg - it reported that cg was incompatible with constraint bonds (LINCS was off, I guess it was about

Re: [gmx-users] print out the velocities and forces using template.c

I think I have found the answer by adding " flags = flags | TRX_READ_V | TRX_READ_F ;". thanks to all. On Sat, Nov 29, 2008 at 12:53 PM, friendli <[EMAIL PROTECTED]> wrote: > I have checked with gmxcheck and velocities and forces are output in .trr. > I am playing template.c to try to learn more