Hi Bharat,
If you have used the -deffnm option then the output gro will be called
whatever name you used for the -deffnm option and not the default
confout.gro.
Tom
Justin A. Lemkul wrote:
bharat gupta wrote:
I didn't gave any -c flag while md run .. and there is no confout.gro in
my folder .. I have attached the graph obtained after energy minimzation
I've never heard of such a thing. mdrun produces several files automatically:
traj.trr, ener.edr, md.log, and confout.gro. The output configuration is always
written. If it wasn't, then something is preventing mdrun from writing this
file (full disk, read/write permissions, etc).
.. I want to ask why the graph is not coming like the one shown in the
tutorial .. I guess I asked that same question earlier also ?? .. Here
is the details of energy minimization result
The shape of the graph is nearly identical. You converged to an acceptable
energy and force, so what's the problem?
If you're following the tutorial's procedure with a different system, there is
absolutely no reason to expect that one system will converge to the same
potential energy as another. They're fundamentally different. Even if you are
working with the same system, there can be differences in the final energy. EM
is just a procedure to optimize the orientation of the molecules in the system.
It may converge somewhat differently each time you do it.
-Justin
Steepest Descents converged to Fmax < 1000 in 720 steps
Potential Energy = -6.7970475e+05
Maximum force = 9.5201904e+02 on atom 78
Norm of force = 1.9553707e+01
On Thu, Jan 27, 2011 at 5:12 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
bharat gupta wrote:
I don't think that there is any problem in the structure ..
since I am simulating the crystal structure taken from PDB ...
and I have checked the structure generated after pdb2gmx and
solvation..
Since I am reapeating the simulation again I want to know and I
am on energy minimzation step I want to know .. how can I
retrieve the structure after minimization ..
The structure after minimization (or any process done by mdrun) is
contained in whatever filename you passed to the -c flag. If you
haven't specified any name, it is confout.gro.
-Justin
On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> wrote:
On 27/01/2011 11:11 PM, bharat gupta wrote:
I used the same .mdp files that are given in the lysozyme
tutorial
.. Since I was knowing what all parameters to change ..
but after
energy minimization and equilibration steps , the graphs
that I
got were fine ... even the rmsd graph of the final
structure is
also fine .. I have attached the final rmsd graph of the
structure ..
That suggests the problem was in the structure you started the
simulation from, like I've suggested a few times now :-)
Mark
On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
bharat gupta wrote:
I generated the secondary structure profile of
structure
retrieved from the last frame of the simulation
... In
that profile those amino acids that are shown as
loops in
VMD doesnot have any secondary structure
assignment ... it
means that during simulation the structure got
changed
some how ... and It's really surprising ?? ...
Can u tell
me where can the fault be as I am planning to do the
simulation again and this time I will check the
structure
after every step .. but for that I want to know
how can I
save the structure after every step say for eg. after
energy minimization ..
Secondary structure is dependent upon the chosen
force field
and the .mdp settings. Since you've posted neither,
there's
no way to tell what might be to blame.
You can save more frequently by setting the proper output
controls. Read in the manual about the nst* options
and set
the accordingly.
-Justin
On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:
Mark Abraham wrote:
On 01/27/11, *bharat gupta *
<bharat.85.m...@gmail.com
<mailto:bharat.85.m...@gmail.com>
<mailto:bharat.85.m...@gmail.com
<mailto:bharat.85.m...@gmail.com>>
<mailto:bharat.85.m...@gmail.com
<mailto:bharat.85.m...@gmail.com>
<mailto:bharat.85.m...@gmail.com
<mailto:bharat.85.m...@gmail.com>>>> wrote:
I actually don't understand exactly
what u are
asking ..
since I am not an expert with gromacs..
Please leave the old context for the
discussion in
future
emails. Only you are paying so much
attention to
your work that
you can be sure of remembering things :-)
If your simulation started with these strands
unfolded, then
your problem is somewhere else. However,
you have
to be able to
tell us what was the initial conformation,
and when
your "first
trajectory frame" (per last email)
happened in the
simulation.
I would also add that VMD does a fairly poor job
sometimes of
guessing secondary structure. So if no beta
strand was
present in
the very first frame, that doesn't necessarily
mean the
secondary
structure wasn't stable, it just means VMD didn't
display it properly.
-Justin
Mark
I don't know when is was written ..
Here are
some lines from
the log files of simulation ...
Statistics over 1500001 steps using
300001 frames
Energies (kJ/mol)
Angle Proper Dih.
Ryckaert-Bell. LJ-14
Coulomb-14
7.35090e+03 4.37413e+02
3.60104e+03 5.26705e+03
2.58894e+04
LJ (SR) Disper. corr.
Coulomb (SR) Coul. recip.
Potential
1.05399e+05 -2.92853e+03
-6.79288e+05 -1.07015e+05
-6.41286e+05
Kinetic En. Total Energy
Temperature
Pres. DC (bar)
Pressure (bar)
1.03484e+05 -5.37802e+05
3.00003e+02 -2.37485e+02
1.02890e+00
Constr. rmsd
0.00000e+00
Box-X Box-Y
Box-Z
7.42618e+00 7.42618e+00
7.42618e+00
Total Virial (kJ/mol)
3.44183e+04 3.40020e+01
-1.17357e+01
3.42160e+01 3.45369e+04
-2.46337e+01
-1.16644e+01 -2.48479e+01
3.44949e+04
Pressure (bar)
1.99809e+00 9.48448e-02
4.57909e-01
7.74354e-02 4.97824e-01
1.84797e+00
4.52125e-01 1.86535e+00
5.90776e-01
Total Dipole (D)
-1.86272e+02 4.46310e+01
2.08554e+02
T-Protein T-non-Protein
2.99904e+02 3.00013e+02
M E G A - F L O P S A C C O U N T I N G
There were in total 1502 frames (as
shown in
VMD )...
I don't know about how it compared
with the
coordinates of
the structure that I gave to grompp
--------
Pls guide
-- Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and
Polymer
Science
Pusan National University
Busan -609735
South Korea
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<mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>> <mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>>>
<mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>> <mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>>>>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/>
<http://vt.edu/> <http://vt.edu <http://vt.edu/>
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Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
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-- ========================================
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/>
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Pusan National University
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========================================
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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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