Re: [gmx-users] S-type Hydrogen bond correlation function
I commented out the 'read_next_x' routine and in place of it i added 'read_next_frame' as given below will that work? Now if i install will i get the trajectory? Is API available for gromacs? Thank you. write_trx(out,natoms,swi,top.atoms,0,t,box,x,NULL); } /* } while(read_next_x(status,t,natoms,x,box)); */ } while(read_next_frame(status,fr)); close_trj(status); if (out != -1) close_trx(out); if (fp) ffclose(fp); thanx(stderr); return 0; } On Mon, Nov 2, 2009 at 9:41 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. It seems likely to be straightforward to change the main loop of gmx_trjorder to use read_next_frame, which will permit it to read and write velocities and forces if they are present. I don't have time to do it, though. Mark On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. First, your .mdp must specify the recording of velocities. Then consult the documentation for trjorder and g_velacc for what you want. Mark On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6,
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: I commented out the 'read_next_x' routine and in place of it i added 'read_next_frame' as given below will that work? You could try it, but it won't work. The whole do...while loop needs to be adjusted to use fr and its struct members, rather than separate box, t, x, etc. Also read_first_frame is required before the loop, not whatever is used there. Now if i install will i get the trajectory? Is API available for gromacs? Thank you. Pre 4.1, API documentation is patchy at best. You can see how this machinery gets used by comparing with the source code of a tool that read and write non-position data, e.g. gmxdump and doubtless others. Obviously, you'll need to recompile and re-install to use any new version. Mark write_trx(out,natoms,swi,top.atoms,0,t,box,x,NULL); } /* } while(read_next_x(status,t,natoms,x,box)); */ } while(read_next_frame(status,fr)); close_trj(status); if (out != -1) close_trx(out); if (fp) ffclose(fp); thanx(stderr); return 0; } On Mon, Nov 2, 2009 at 9:41 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. It seems likely to be straightforward to change the main loop of gmx_trjorder to use read_next_frame, which will permit it to read and write velocities and forces if they are present. I don't have time to do it, though. Mark On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. First, your .mdp must specify the recording of velocities. Then consult the documentation for trjorder and g_velacc for what you want. Mark On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047
Re: [gmx-users] S-type Hydrogen bond correlation function
Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. Regards, Rama On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. First, your .mdp must specify the recording of velocities. Then consult the documentation for trjorder and g_velacc for what you want. Mark On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it
Re: [gmx-users] S-type Hydrogen bond correlation function
Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. Thanks. Rama On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. First, your .mdp must specify the recording of velocities. Then consult the documentation for trjorder and g_velacc for what you want. Mark On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. It seems likely to be straightforward to change the main loop of gmx_trjorder to use read_next_frame, which will permit it to read and write velocities and forces if they are present. I don't have time to do it, though. Mark On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. First, your .mdp must specify the recording of velocities. Then consult the documentation for trjorder and g_velacc for what you want. Mark On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter
Re: [gmx-users] S-type Hydrogen bond correlation function
Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing list
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
Re: [gmx-users] S-type Hydrogen bond correlation function
Thank you. Since i am using gromacs version 3.3.1 i facing the problem in getting the trajectory output with the option -r as given in the thread, http://www.mail-archive.com/gmx-users@gromacs.org/msg01629.html Is there any alternative way to solve the problem... rama On Sun, Nov 1, 2009 at 12:43 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] S-type Hydrogen bond correlation function
I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group,
[gmx-users] S-type Hydrogen bond correlation function
Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] S-type Hydrogen bond correlation function
Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] S-type Hydrogen bond correlation function
Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: C_HB(T) = h(t)h(T+t)/ h(t) S_HB(T) = h(t)H(T+t)/h(t) h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, otherwise S_HB(t) probes the continuous existence of a hydrogen bond, while C_HB(t) allows for the reformation of a bond that is broken at some intermediate time. The former is thus a strict definition of the hydrogen bond lifetime, while the latter is more permissive. I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure about that. Anybody knows please help me. Thank you. This is correct. However, the S_HB definition is not very useful, see my paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The uninterrupted life time is computed by g_hbond however. Check the screen output. Rama On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing list gmx-us...@gromacs.org
