Antw: Re: Re: Antw: Re: [gmx-users] Hydrogen existence time
The number of frames is in your mdp-file. nstxout = frequency of output (timestep when it writes out one frame) dt = timestep time of frame = number_of_frame * nstxout * dt With programming you have to learn one certain programming-language. I cannot help you with learning programming - this at least you have to do yourself. >>what programming should be applied and what for I would suggest you to learn C or Fortran-coding. You also could use a script-language, like bash. A theoretician must be able to do some little programming. If you want to do that 1000.000 times by hand, you can do it. You also could integrate the equations of motion by hand for your trajectory. >>> aiswarya pawar 25.08.11 10.54 Uhr >>> Dear Emanuel, Thank you so much for the pseudo-code, it made me understand the flow. from your code it shows that, your using distance and angle as an criteria to select a water molecule in just one one time frame. right?? i didnt get how to calculate the time of the frame. what programming should be applied and what for. Thanks, Aiswarya On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter wrote: Hello Aiswarya, Your program should look like this, in pseudo-code: pseudo-code: do n_frames_of_your_trajectory g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent (second-group)).ndx -o atm-pair.out -d your-distance-value -b (one frame of your trajectory) -e (the same frame) processing the atm-pair.out list and write them into an index file : 1.ndx, with each water in one group take just these atoms and residues, which are at your specific distance at your 'location' do measure the angle in relation to your protein for this frame for each specified water g_angle -f traj.trr -s .tpr -n 1.ndx -b (one frame of your trajectory) -e (the same frame) enddo read the angles from the output take just the one water with specific angle out of your list. (By using g_mindist -d , and g_angle you specify one specific point in relation to your protein) (By using -b and -e you specify one specific time) save the residue number of this water and your frame calculate the time of this frame enddo now you have an array of residue numbers at this particular location for each time analyse this array, then you know the maximum frame-time of one water-molecule at this specific location. You will not get any information about one particular time - just an average. This must be your residence time. Your application needs some little programming. >>> 24.08.11 18.14 Uhr >>> Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 + To: Gromacs mail ReplyTo: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: "Emanuel Peter" Date: Wed, 24 Aug 2011 16:16:37 +0200 To: ; Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. >>> 24.08.11 16.01 Uhr >>> Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculat
Re: Re: Antw: Re: [gmx-users] Hydrogen existence time
Dear Emanuel, Thank you so much for the pseudo-code, it made me understand the flow. from your code it shows that, your using distance and angle as an criteria to select a water molecule in just one one time frame. right?? i didnt get how to calculate the time of the frame. what programming should be applied and what for. Thanks, Aiswarya On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter < emanuel.pe...@chemie.uni-regensburg.de> wrote: > Hello Aiswarya, > > Your program should look like this, in pseudo-code: > > pseudo-code: > > do n_frames_of_your_trajectory > > g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent > (second-group)).ndx -o atm-pair.out -d your-distance-value -b (one frame of > your trajectory) -e (the same frame) > > processing the atm-pair.out list and write them into an index file : 1.ndx, > with each water in one group > > take just these atoms and residues, which are at your specific distance at > your 'location' > > do > > measure the angle in relation to your protein for this frame for each > specified water > > g_angle -f traj.trr -s .tpr -n 1.ndx -b (one frame of your trajectory) -e > (the same frame) > > enddo > > read the angles from the output > > take just the one water with specific angle out of your list. > > (By using g_mindist -d , and g_angle you specify one specific point in > relation to your protein) > (By using -b and -e you specify one specific time) > > save the residue number of this water and your frame > > calculate the time of this frame > > enddo > > now you have an array of residue numbers at this particular location for > each time > > analyse this array, then you know the maximum frame-time of one > water-molecule at this specific location. > You will not get any information about one particular time - just an > average. > This must be your residence time. > > Your application needs some little programming. > > > >>> ** 24.08.11 18.14 Uhr >>> > Emanuel, > > The residence time which am referring is the water molecule residing on the > particular location at a specific time. > > Am not able to write a correct equation due to some character missing when > typing from phone. > > Aiswarya > > Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for > it! > -- > *From: * aiswarya.pa...@gmail.com > *Date: *Wed, 24 Aug 2011 16:13:05 + > *To: *Gromacs mail > *ReplyTo: * aiswarya.pa...@gmail.com > *Subject: *Re: Antw: Re: [gmx-users] Hydrogen existence time > > Emanuel, > > The residence time which am referring is the water molecule residing on the > particular location at a specific time. > > Am not able to write a correct equation due to small character missing when > typing from phone. > > Aiswarya > > Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for > it! > -- > *From: * "Emanuel Peter" > *Date: *Wed, 24 Aug 2011 16:16:37 +0200 > *To: *; > *Subject: *Antw: Re: [gmx-users] Hydrogen existence time > > As I told you, you can calculate the self-diffusion coefficient by using > g_msd. > Following: > > Large diffusion-coeff. --> means : The residence time is low. > Small diffusion-coeff. --> means : The residence time is large > > Mean-square-displacement means: Displacement of molecules per time. > No displacement of molecule at all : if(msd == 0) means: Infinite > residence time. > So I say from my idiotic point of view: msd ~ residence time ( I still do > not know what you mean with this because > this is usually related to chemical reactors in engineering and NOT in > protein simulation ) > In your index-file you can index those molecules, which you need. > Your equation does not make sense. > > >>> 24.08.11 16.01 Uhr >>> > Mark, > > The residence time equation goes like this- > > P(r)= function (N(t) - N(t+r))dt > > Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y > not equal to 0) ie the site occupied and when x not equal to y or both x and > y =0. N(t) index of water molecule found in the hydration site at time t. > > Aiswarya > --Original Message-- > From: Mark Abraham > To: Aiswarya Pawar > Subject: Re: [gmx-users] Hydrogen existence time > Sent: 24 Aug 2011 6:09 PM > > On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: > > Any idea how can I calculate the residence time of water. > > First, seek define what you mean to calculate. If you can't write an > equation down for it, you can't calculate it. > > Mark > > Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for > it!** > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Antw: Re: Antw: Re: [gmx-users] Hydrogen existence time
Hello Aiswarya, Your program should look like this, in pseudo-code: pseudo-code: do n_frames_of_your_trajectory g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent (second-group)).ndx -o atm-pair.out -d your-distance-value -b (one frame of your trajectory) -e (the same frame) processing the atm-pair.out list and write them into an index file : 1.ndx, with each water in one group take just these atoms and residues, which are at your specific distance at your 'location' do measure the angle in relation to your protein for this frame for each specified water g_angle -f traj.trr -s .tpr -n 1.ndx -b (one frame of your trajectory) -e (the same frame) enddo read the angles from the output take just the one water with specific angle out of your list. (By using g_mindist -d , and g_angle you specify one specific point in relation to your protein) (By using -b and -e you specify one specific time) save the residue number of this water and your frame calculate the time of this frame enddo now you have an array of residue numbers at this particular location for each time analyse this array, then you know the maximum frame-time of one water-molecule at this specific location. You will not get any information about one particular time - just an average. This must be your residence time. Your application needs some little programming. >>> 24.08.11 18.14 Uhr >>> Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 + To: Gromacs mail ReplyTo: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: "Emanuel Peter" Date: Wed, 24 Aug 2011 16:16:37 +0200 To: ; Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. >>> 24.08.11 16.01 Uhr >>> Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Antw: Re: Antw: Re: [gmx-users] Hydrogen existence time
Good luck >>> 24.08.11 18.14 Uhr >>> Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 + To: Gromacs mail ReplyTo: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! From: "Emanuel Peter" Date: Wed, 24 Aug 2011 16:16:37 +0200 To: ; Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. >>> 24.08.11 16.01 Uhr >>> Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Antw: Re: [gmx-users] Hydrogen existence time
Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 To: Gromacs mail Reply-To: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: "Emanuel Peter" Date: Wed, 24 Aug 2011 16:16:37 To: ; Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. >>> 24.08.11 16.01 Uhr >>> Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Antw: Re: [gmx-users] Hydrogen existence time
Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: "Emanuel Peter" Date: Wed, 24 Aug 2011 16:16:37 To: ; Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. >>> 24.08.11 16.01 Uhr >>> Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Antw: Re: [gmx-users] Hydrogen existence time
As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. >>> 24.08.11 16.01 Uhr >>> Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t. Aiswarya --Original Message-- From: Mark Abraham To: Aiswarya Pawar Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 6:09 PM On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the residence time of water. First, seek define what you mean to calculate. If you can't write an equation down for it, you can't calculate it. Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Antw: Re: [gmx-users] Hydrogen existence time
Dear Emanuel, Iam following what you have mentioned earlier. But as you said hydrogen bond correlation time gives the average hydrogen bond existence time. So I confused understanding whether an H Bond existence time would give me the residence time. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: "Emanuel Peter" Sender: gmx-users-boun...@gromacs.org Date: Wed, 24 Aug 2011 15:42:11 To: ; Reply-To: Discussion list for GROMACS users Subject: Antw: Re: [gmx-users] Hydrogen existence time -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Antw: Re: [gmx-users] Hydrogen existence time
You do not know, what you are doing as I suppose. I suggested you already to calculate the H-bond correlation time, or the self-diffusion coefficient of this specific molecule. >>> "Justin A. Lemkul" 24.08.11 15.04 Uhr >>> aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the residence time of water. > There have been recent discussions on this topic, so please check the archive. The solution is an external program that one of the users provided; there are no Gromacs tools that will do this. -Justin > Aiswarya > --Original Message-- > From: Justin A. Lemkul > To: Aiswarya Pawar > To: Gromacs mail > ReplyTo: jalem...@vt.edu > Subject: Re: [gmx-users] Hydrogen existence time > Sent: 24 Aug 2011 5:58 PM > > > > aiswarya.pa...@gmail.com wrote: >> Dear Justin, >> >> So what does the hydrogen bond existence state? >> > > The length of time for which a given hydrogen bond exists (i.e. satisfies the > geometrical criteria in the context of some particular partner group). > > -Justin > >> Thanks >> --Original Message-- >> From: Justin A. Lemkul >> To: Aiswarya Pawar >> To: Gromacs mail >> ReplyTo: jalem...@vt.edu >> Subject: Re: [gmx-users] Hydrogen existence time >> Sent: 24 Aug 2011 5:54 PM >> >> >> >> aiswarya.pa...@gmail.com wrote: >>> Dear all, >>> >>> Does Hydrogen bond existence in a time frame states the residence time of >>> the water molecule? >>> >> Not necessarily, no. >> >> -Justin >> >> > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
