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 time 0.000
Will do grid-seach on 16x16x16 grid, rcut=0.35
Last frame 30000 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
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
+4618511755.
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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
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
+4618511755.
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