Re: [gmx-users] malloc on mac

2011-08-02 Thread Sara baretller
do you suggest any other way to find the hbond?? is the cut of distance of 3 or less something i can do in this case or not?? thank you On Tue, Aug 2, 2011 at 1:58 PM, Justin A. Lemkul wrote: > > > Sara baretller wrote: > >> >> does the g_hbond work for course grained file. i tried this command

Re: [gmx-users] malloc on mac

2011-08-02 Thread Tsjerk Wassenaar
Hi Sara, Since you don't have hydrogens, it's hard to talk about hydrogen bonds according to conventional criteria. Note this has nothing to do with malloc; please start a new thread rather than asking your question in another. Cheers, Tsjerk On Aug 2, 2011 7:56 PM, "Sara baretller" wrote:

Re: [gmx-users] malloc on mac

2011-08-02 Thread Justin A. Lemkul
Sara baretller wrote: does the g_hbond work for course grained file. i tried this command and it gave me nothing but an error it does not matter wich selection If there are no hydrogens, there is nothing for g_hbond to measure. You need an atomistic representation such that D-H-A angle

Re: [gmx-users] malloc on mac

2011-08-02 Thread Sara baretller
does the g_hbond work for course grained file. i tried this command and it gave me nothing but an error it does not matter wich selection On Tue, Aug 2, 2011 at 1:01 PM, Justin A. Lemkul wrote: > > > Sara baretller wrote: > >> I have a question about the g-hbond selection . after i typed in th

Re: [gmx-users] malloc on mac

2011-08-02 Thread Justin A. Lemkul
Sara baretller wrote: I have a question about the g-hbond selection . after i typed in the g_hbond , it asked me to choose two groops and i am wondering what is difference between Protein and Protein-H ? http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups -Justin Thank

Re: [gmx-users] malloc on mac

2011-08-02 Thread Sara baretller
I have a question about the g-hbond selection . after i typed in the g_hbond , it asked me to choose two groops and i am wondering what is difference between Protein and Protein-H ? Thank you Specify 2 groups to analyze: Group 0 ( System) has 7722 elements Group 1 (Protei

Re: [gmx-users] malloc on mac

2011-07-14 Thread Mark Abraham
On 15/07/2011 11:48 AM, Itamar Kass wrote: Hi all, I am trying to find all possible h-bonds between chains in my complex. I am using: g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n system.ndx -g system_run1_MD050_fitbb_Hbond_all.log -num system_run1_MD050_fitbb_Hbnum_all.x

[gmx-users] malloc on mac

2011-07-14 Thread Itamar Kass
Hi all, I am trying to find all possible h-bonds between chains in my complex. I am using: g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n system.ndx -g system_run1_MD050_fitbb_Hbond_all.log -num system_run1_MD050_fitbb_Hbnum_all.xvg -hbn system_run1_MD050_fitbb.xtc_Hbond_a