[gmx-users] Removing relative motion of water
Dear all: I'm trying to use g_densmap to analyze densities of water, but the result seems to be blurry due to relative motion (?). Does anyone have any suggestions on how to solve this problem? Thanks in advance. Happy holidays! Best, Wei-Hsiang -- Wei-Hsiang Weng (翁偉翔) Department of Life Sciences Tzu-Chi University No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan Tel.: +886-975-232-245 -- 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] gmx bundle
Dear all: I'm trying to calculate kinks within alpha helices using gmx bundle. I specify 4 Ca atoms from the helix top, bottom and kink separately in the index file. And, I've used the option -na 1. But I keep getting the results shown below. @title "Kink angles" @xaxis label "Time (ps)" @yaxis label "(degrees)" @TYPE xy 0 -nan 500 -nan 1000 -nan 1500 -nan 2000 -nan 2500 -nan 3000 -nan 3500 -nan 4000 -nan 4500 -nan 5000 -nan ... ... Does anyone know what "-nan" implies? Any advice would be appreciated, thanks in advance. Best, Wei-Hsiang -- Wei-Hsiang Weng (翁偉翔) Department of Life Sciences Tzu-Chi University No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan Tel.: +886-975-232-245 -- 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] g_correlation
Hi Dr. Bowerman: Thanks for replying. Happy holidays! Best, Wei-Hsiang -- Wei-Hsiang Weng (翁偉翔) Department of Life Sciences Tzu-Chi University No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan Tel.: +886-975-232-245 2016-01-26 11:18 GMT+08:00 Samuel Bowerman : > Hello Wei-Hsiang, > > G_correlation will print a 0-1 value automatically. If you provide the > "-mi" flag, then the output is raw mutual information (range 0 to > infinity). You can not "set a range" for the values; they are what they > naturally are. You simply choose what formalism to work in (correlation > coefficient vs. MI value). Any filtering of values is a matter of > post-processing. > > Take care, > Samuel Bowerman > Ph.D. Candidate > Illinois Institute of Technology > On Jan 25, 2016 9:14 PM, "Felix W.-H. Weng" wrote: > > > Dear all: > > > > I'm using the generalized correlation analysis tool developed by Lange > and > > Grubmüller. Does anyone know the option for setting the range of > > correlation values? Say, 0 to 1? > > > > Any advice would be appreciated, thanks in advance. > > > > Best, > > Wei-Hsiang > > -- > > Wei-Hsiang Weng (翁偉翔) > > Department of Life Sciences > > Tzu-Chi University > > No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan > > Tel.: +886-975-232-245 > > -- > > 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. -- 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] g_correlation
Dear all: I'm using the generalized correlation analysis tool developed by Lange and Grubmüller. Does anyone know the option for setting the range of correlation values? Say, 0 to 1? Any advice would be appreciated, thanks in advance. Best, Wei-Hsiang -- Wei-Hsiang Weng (翁偉翔) Department of Life Sciences Tzu-Chi University No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan Tel.: +886-975-232-245 -- 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] g_correlation
Hi, Thank you for your patience. It seems that statutil.h is missing under both locations... I do see a stringutil.h under /usr/local/gromacs/include/gromacs/utility though, could that be used as a replacement for GROMACS 4.5.5? Best, Wei-Hsiang >>>>>>>>>>>>>>>>>>>>>>>>>>> Wei-Hsiang Weng (翁偉翔), Master Department of Life Sciences Tzu-Chi University, Taiwan 0975-232-245 (C) E-mail: weiweng...@gmail.com 104726...@gms.tcu.edu.tw 2015-12-10 16:45 GMT+08:00 Kutzner, Carsten : > Hi, > > > On 10 Dec 2015, at 08:59, Felix W.-H. Weng wrote: > > > > Dear all: > > > > Has anyone succeeded in installing the command g_correlation in GROMACS > > 4.5.5? > Does it work with 3.3? > > > File obtained from http://www.mpibpc.mpg.de/grubmueller/g_correlation > > I tried installing but I keep getting the error message seen below. > > > > *6/include -I/usr/local/gromacs/bin/include/gromacs -c -o g_correlation.o > > g_correlation.c g_correlation.c:40:42: fatal error: statutil.h: No such > > file or directory* > > *#include statutil.h* > Is your 4.5.5 statutil.h. in /usr/local/gromacs/bin/include/gromacs/ or is > it in /usr/local/gromacs/include/gromacs/ ? > > You will likely need to adapt the g_correlation code a bit, though. > > Carsten > > > > > *compilation terminated.* > > *make: *** [g_correaltion.o] Error 1* > > > > Does anyone have any suggestions? Thanks. > > -- > > 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. > -- 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] g_correlation
Dear all: Has anyone succeeded in installing the command g_correlation in GROMACS 4.5.5? File obtained from http://www.mpibpc.mpg.de/grubmueller/g_correlation I tried installing but I keep getting the error message seen below. *6/include -I/usr/local/gromacs/bin/include/gromacs -c -o g_correlation.o g_correlation.c g_correlation.c:40:42: fatal error: statutil.h: No such file or directory* *#include statutil.h* *compilation terminated.* *make: *** [g_correaltion.o] Error 1* Does anyone have any suggestions? Thanks. -- 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.
