Re: [gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch
Thanks David for the clarifications. I really appreciate it.Atanu On Friday, 13 March 2015 2:07 AM, David van der Spoel sp...@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 samr...@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 sp...@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 samr...@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. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch
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 samr...@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 sp...@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 samr...@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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch
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 samr...@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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch
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)) ThanksAtanu On Wednesday, 11 March 2015 9:13 PM, atanu das samr...@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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch
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 On Thursday, 12 March 2015 6:12 PM, atanu das samr...@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 behavior. 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 sp...@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 samr...@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. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch
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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
