[gmx-users] phi / psi values using g_chi

[XAvier Periole]

Your answer was very useful! I actually could point out where the
"confusion" came from!

Thanks,
XAvier.

On Mar 11, 2009, at 10:43 PM, chris.neale at utoronto.ca wrote:

> I was either using using 3.3 or 3.3.1, certainly not 3.1.4 or 3.2.1.
>
> It looks like the change was in 3.3.1, possibly by Erik:
>
> [tera:~]?diff gromacs-3.3/src/tools/gmx_chi.c gromacs-3.3.1/src/ 
> tools/gmx_chi.c
> 2c2
> <  * $Id: gmx_chi.c,v 1.3 2005/02/16 17:39:27 hess Exp $
> ---
>> * $Id: gmx_chi.c,v 1.3.2.2 2006/04/02 15:09:37 lindahl Exp $
> 148,172c148,170
> <   for(i=0; (i<nl); i++) { /* Phi */
> <     dl[i].j0[edPhi] = n/4;
> <     if (dl[i].atm.H == -1)
> <       id[n++]=dl[i].atm.minC;
> <     else
> <       id[n++]=dl[i].atm.H;
> <     id[n++]=dl[i].atm.N;
> <     id[n++]=dl[i].atm.Cn[1];
> <     id[n++]=dl[i].atm.C;
> <   }
> <   for(i=0; (i<nl); i++) { /* Psi */
> <     dl[i].j0[edPsi] = n/4;
> <     id[n++]=dl[i].atm.N;
> <     id[n++]=dl[i].atm.Cn[1];
> <     id[n++]=dl[i].atm.C;
> <     id[n++]=dl[i].atm.O;
> <   }
> <   for(i=0; (i<nl); i++) { /* Omega */
> <     if (has_dihedral(edOmega,&(dl[i]))) {
> <       dl[i].j0[edOmega] = n/4;
> <       id[n++]=dl[i].atm.minO;
> <       id[n++]=dl[i].atm.minC;
> <       id[n++]=dl[i].atm.N;
> <       id[n++]=dl[i].atm.Cn[1];
> <     }
> ---
>>  for(i=0; (i<nl); i++)   {
>>        /* Phi, fake the first one */
>>        dl[i].j0[edPhi] = n/4;
>>        if(dl[i].atm.minC >= 0)
>>                id[n++]=dl[i].atm.minC;
>>        else
>>                id[n++]=dl[i].atm.H;
>>        id[n++]=dl[i].atm.N;
>>        id[n++]=dl[i].atm.Cn[1];
>>        id[n++]=dl[i].atm.C;
>>  }
>>  for(i=0; (i<nl); i++)   {         /* Psi, fake the last one */
>>        dl[i].j0[edPsi] = n/4;
>>        id[n++]=dl[i].atm.N;
>>        id[n++]=dl[i].atm.Cn[1];
>>        id[n++]=dl[i].atm.C;
>>        if ( i< (nl-1) )
>>                id[n++]=dl[i+1].atm.N;
>>        else
>>                id[n++]=dl[i].atm.O;
> ...
> <snip>
>
> Note that I am not sure if 3.3.1 will give you what you expect for  
> the terminal residues, even if they are capped. I suspect that it  
> will not.
>
> In the link that I mentioned earlier, I discuss "...plot the  
> dih.rest. energy
> output from g_energy and scatter plot this with the actual dihedral  
> value from
> g_chi for a particular umbrella". If there is scatter from the  
> expected energy
> function then you may suspect that g_chi is still incorrect.
>
> I switched to g_rama for my work and never looked back, so don't  
> take my word for it that g_chi is correct now, I just took a really  
> quick look.
>
> Chris.
>
> -- original message --
>
> Hi Chris,
>
> Thanks for the link.
>
> I then do not understand what is happening because I get the same
> exact values
> with g_chi and g_rama! Are you sure you were using the gmx-3.3.1? And
> not an
> earlier version?
>
> Note that in the code of gmx-3.1.4 and gmx-3.2.1 the non-standard
> definition is used
> but in the gmx-3.3.1 the code is changed and the standard definition
> is used.
>
> Anyone would have changed the code and forgot to update the comment on
> the
> choice of the atoms to calculate the phi/psi angles in g_chi ?
>
> XAvier.
> ---------------------
> Data:
> g_chi / from the phi-psi files for Ala15
> 10000 -112.924 42.8174
> 10100 -114.15 57.1768
> 10200 -82.0442 -11.6453
> 10300 -99.8691 36.5998
> 10400 -83.1319 -20.2397
> g_rama / extracting the Ala15 data
> 10000 -112.924  42.8174  ALA-15
> 10100 -114.15  57.1768  ALA-15
> 10200 -82.0442  -11.6453  ALA-15
> 10300 -99.8691  36.5998  ALA-15
> 10400 -83.1319  -20.2397  ALA-15
> 10500 -104.275  12.6959  ALA-15
>
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