Re: [gmx-users] correlation function 'time value' ?

Dear Mark and David, Thanks you, i will check the paper very carefully and try again. regards, Rama On Sat, Feb 27, 2010 at 1:13 AM, Mark Abraham wrote: > On 27/02/2010 7:31 PM, Ramachandran G wrote: > >> Dear Dr. van der Spoel: >> >> Thanks for the clarification in your reply. One more

Re: [gmx-users] correlation function 'time value' ?

On 27/02/2010 7:31 PM, Ramachandran G wrote: Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = < f(x).f(x+t) >, what is the default value for t, which is often called "correlation time", in gromacs for correlation function c

Re: [gmx-users] correlation function 'time value' ?

On 2010-02-27 09.31, Ramachandran G wrote: Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = < f(x).f(x+t) >, what is the default value for t, which is often called "correlation time", in gromacs for correlation function cal

Re: [gmx-users] correlation function 'time value' ?

Dear Dr. van der Spoel: Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = < f(x).f(x+t) >, what is the default value for t, which is often called "correlation time", in gromacs for correlation function calculation, especially in "g_hbond", and/or is

Re: [gmx-users] correlation function 'time value' ?

On 2010-02-27 03.27, Ramachandran G wrote: Hi gromacs users: As you know autocorrelation function C(t) C(t) = 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank

[gmx-users] correlation function 'time value' ?

Hi gromacs users: As you know autocorrelation function C(t) C(t) = 't' value can start from 0 but, i would like to know what value does gromacs use, more specifically for g_hbond. Can anyone help me? Thank you. Rama -- gmx-users mailing list

Re: [gmx-users] correlation function

Jamie Seyed wrote: On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul > wrote: Jamie Seyed wrote: with a lot of x-y sets seperated by & character. I think I did not get the key point here. So my question is what is the right way to get

Re: [gmx-users] correlation function

On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul wrote: > > > Jamie Seyed wrote: > > with a lot of x-y sets seperated by & character. I think I did not get the >> key point here. So my question is what is the right way to get >> using this tool?? Many Thanks/Jamie >> > > Well, as far as g_analy

Re: [gmx-users] correlation function

Jamie Seyed wrote: with a lot of x-y sets seperated by & character. I think I did not get the key point here. So my question is what is the right way to get using this tool?? Many Thanks/Jamie Well, as far as g_analyze is concerned, it's done its job. If you feed g_analyze a whole bunch

Re: [gmx-users] correlation function

On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul wrote: > > > >Actually when I open autocorr.xvg I can see from data/feature >>extraction/ the last set is S1295 (N=101, autocorr.xvg) which means >>they are 1296 graphs each with poor statistics start at 1 and coming >>down. To ha

Re: [gmx-users] correlation function

Actually when I open autocorr.xvg I can see from data/feature extraction/ the last set is S1295 (N=101, autocorr.xvg) which means they are 1296 graphs each with poor statistics start at 1 and coming down. To have a ACF for a system I expect to get one graph with good stati

Re: [gmx-users] correlation function

On Sun, Aug 23, 2009 at 10:30 AM, Jamie Seyed wrote: > Hi Justin, > Thanks for the answers. Please check below... > > On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul wrote: > > >>> >>> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote: >>> >>> >>> >>>Jamie Seyed

Re: [gmx-users] correlation function

Hi Justin, Thanks for the answers. Please check below... On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul wrote: >> >> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Jamie Seyed wrote: >> >>Hi Justin and Mark, >>Thanks. Actually I ma

Re: [gmx-users] correlation function

Jamie Seyed wrote: On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul > wrote: Jamie Seyed wrote: Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I can write my command to get only one graph (average of all instead of all of them). I read the manual chapter-8 and by average I mean I should get

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I can write my command to get only one graph (average of all instead of all of them). I read the manual chapter-8 and by average I mean I should

Re: [gmx-users] correlation function

Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I can write my command to get only one graph (average of all instead of all of them). I read the manual chapter-8 and by average I mean I should get one curve starting at

Re: [gmx-users] correlation function

Justin A. Lemkul wrote: Jamie Seyed wrote: Hi Justin, Thanks again. I made and used coord.xvg with command g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Huh? The average has nothing to do with calculating the autocorrelation func

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin, Thanks again. I made and used coord.xvg with command g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Would you please let me know how I can get a nice average curve? Also I can see that all of them starti

Re: [gmx-users] correlation function

Hi Justin, Thanks again. I made and used coord.xvg with command g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Would you please let me know how I can get a nice average curve? Also I can see that all of them starting at 1, but I do not thi

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin, Thanks for the answer. I want to calculate auto-correlation function of R(x,y,z). I mean , .../Many Thanks in Advance/Jamie Coordinates? Use g_traj. -Justin On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul > wrote: Jamie Se

Re: [gmx-users] correlation function

Hi Justin, Thanks for the answer. I want to calculate auto-correlation function of R(x,y,z). I mean , .../Many Thanks in Advance/Jamie On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul wrote: > > > Jamie Seyed wrote: > >> Hi Mark, >> Thanks for the answers. I want to use g_analyze but it needs

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Mark, Thanks for the answers. I want to use g_analyze but it needs a file graph.xvg as an input file. How can I get that for calculation of auto-correlation function? Many Thanks in Advance/Jamie The graph.xvg file contains the data for which you want to obtain the

Re: [gmx-users] correlation function

Hi Mark, Thanks for the answers. I want to use g_analyze but it needs a file graph.xvg as an input file. How can I get that for calculation of auto-correlation function? Many Thanks in Advance/Jamie On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham wrote: > Jamie Seyed wrote: > >> Hi Mark, >> Thanks

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Mark, Thanks for the information. Actually in 7.4 I found only g_rotacf and g_angle also g_sgangle that calculate rotation and angle correlation function and in appendix D I could not find related topic... I appreciate if someone gives me more detail to do the job. I want to

Re: [gmx-users] correlation function

Hi Mark, Thanks for the information. Actually in 7.4 I found only g_rotacf and g_angle also g_sgangle that calculate rotation and angle correlation function and in appendix D I could not find related topic... I appreciate if someone gives me more detail to do the job. I want to calculate that R is

Re: [gmx-users] correlation function

Jamie Seyed wrote: Dear all, Is there any tool in gromacs that can calculate time correlation function ??? R(x,y,z). Many Thanks in Advance/Jamie Yes, various tools can calculate (auto)correlation functions. See manual section 7.4 and appendix D. Mark ___

[gmx-users] correlation function

Dear all, Is there any tool in gromacs that can calculate time correlation function ??? R(x,y,z). Many Thanks in Advance/Jamie ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi