[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch

[atanu das]

Thanks David for the clarifications. I really appreciate it.Atanu 

     On Friday, 13 March 2015 2:07 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
   

 On 2015-03-13 00:30, atanu das wrote:
> Hi David, I have checked both the codes, g_angle.c and g_chi.c, and the same Cos function is used in both the cases (please correct me if I am wrong).  g_angle analysis: I have used the following command to calculate the average autocorrelation function (ACF) over all the backbone phi & psi dihedral angles given in the index file. The phi-psi definition I use in the index file is the usual description of dihedral angles i.e. C-N-CA-C and N-CA-C-N. g_angle -f final.xtc -n phi-psi.ndx -oc dihcorr.xvg -type dihedral -avercorr g_chi analysis: I have used the following command to estimate the autocorrelation function of individual dihedral angles and then estimated the average autocorrelation function to compare with the previous result.  g_chi -s md.tpr -f final.xtc -corr -phi -psi
> The two curves (average ACFs calculated by two procedure) show almost similar behavior (tried to attach the figure file, but couldn't due to size limit). The slightly faster relaxation time obtained from g_chi may be attributed to the phi-psi description in-built in g_chi analysis (H-N-CA-C and N-CA-C-O).
>  Is there a way to calculate ACF using the formula you described in your Biophysical Journal 97 article (Eq. 1)? ThanksAtanu
>

I think g_chi does exactly that.

>
>      On Thursday, 12 March 2015 6:12 PM, atanu das <samrucu at yahoo.co.in> wrote:
>
>
>  HiDavid,  Ihave checked both the codes, g_angle.c and g_chi.c, and the same Cos function is usedin both the cases (please correct me if I am wrong). I am sending this figureto you (to all others) to explain my approach clearly.  Ihave simulated the system for 1 microsecond and chosen the default i.e. half ofthe simulations length (500 ns) for ACF analysis.  g_angleanalysis: I have used the following command to calculate the averageautocorrelation function (ACF) over all the backbone phi & psi dihedralangles given in the index file. The phi-psi definition I used in the index fileis the usual description of dihedral angles i.e. C-N-CA-C and N-CA-C-N.  g_angle-f final.xtc -n phi-psi.ndx -oc dihcorr.xvg -type dihedral -avercorr  g_chianalysis: I have used the following command to estimate the autocorrelationfunction of individual dihedral angles and then estimated the averageautocorrelation function to compare with the previous result. The two curvesshow almost similar beha
 vior. The
 slightly faster relaxation time obtained fromg_chi (green line) may be attributed to the phi-psi description in-built in g_chianalysis (H-N-CA-C and N-CA-C-O)  g_chi-s md.tpr -f final.xtc -corr -phi -psi  Isthere a way to calculate ACF using the formula you described in your BiophysicalJournal 97 article (Eq. 1)?  ThanksAtanu
>
>      On Thursday, 12 March 2015 2:19 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
>
>  On 2015-03-12 19:03, atanu das wrote:
>> Hi again,
>> Just to add a note ---
>> It seems that g_angle can also calculate the dihedral angle autocorrelation function with the option -oc. Does this program use the same functional form as g_chi i.e. is the functions defined as ---
>> C(t) = <cos(theta(tau)) cos(theta(tau+t)) >
> I don't think so, but please check the source code if unsure.
>> ThanksAtanu
>>
>>        On Wednesday, 11 March 2015 9:13 PM, atanu das <samrucu at yahoo.co.in> wrote:
>>
>>
>>    Hi All,
>> As Prof. David van der Spoel referred in the last communication about how the dihedral angle autocorrelation function is calculated via the program g_chi, I have a query regarding the differences that I found between the function mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function used by the program g_chi.
>> According to the article, the dihedral angle autocorrelation function is defined as:
>> C(t) = <cos[theta(tau)-theta(tau+t)]> ..... (Eq. 1 of the article)
>>
>> However, the g_chi program uses the function:
>> C(t) = <cos(theta(tau)) cos(theta(tau+t)) > ..... (Eq. 2)
>> So, apparently the g_chi program uses a different function. Am I correct? Is there a way around it? I mean is there a way to estimate C(t) using the function given in the article (Eq. 1)?
>> ThanksAtanu
>>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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