Regards
Vinoth
On Thu, Oct 21, 2010 at 5:25 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
vinothkumar mohanakrishnan wrote:
Hi Justin
Below is my nvt.mdp (nvt equilibration) file.i think probably
you can have look at it and its not such big.
define = -DFLEXIBLE
You should never run MD with flexible water. All the water models
included in Gromacs are meant to be rigid. -DFLEXIBLE should only
be used during EM.
integrator = md nsteps =
50000 dt =
0.002 nstxout = 100 nstvout
= 100 nstenergy =
100 nstlog = 100
constraint_algorithm = shake constraints =
none
If you're not using constraints, then a 2-fs timestep might be too
large. If you encounter any later instability, this is likely the
cause.
unconstrained_start = yes shake_tol =
0.0001
morse = no ns_type =
grid nstlist = 5
rlist = 1.0 coulombtype =
PME rcoulomb = 1.0
vdwtype = Cut-off rvdw =
1.0 pme_order = 4
fourierspacing = 0.16 pbc =
xyz tcoupl = V-rescale
tc-grps = system tau_t =
0.1 ref_t = 300
DispCorr = Ener gen_vel =
yes gen_temp = 300 gen_seed =
173529
regarding the plot i too know that one should use Xmgrace to
plot. In the pressure Vs time(lysozyme tutorial) you have got
two graphs. i to got the pressure Vs time (black line graph) my
question is how to get the running average ( red line) and
plot?. does i need any command to get the running average?. any
help is highly appreciated.
Data -> Transformations -> Running averages
-Justin
Regards
Vinoth
On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
vinothkumar mohanakrishnan wrote:
Hi justin
I found what went wrong and i corrected my mdp file.now the
system equilibrated to the desired temperature 300 K (plus r
minus 30 K) is this ok?
This is impossible to assess without seeing your .mdp
settings. A
fluctuation of 10% is probably fine.
Apart from that i want to know how you plot the average
running
pressure and density in your tutorial for lyzosyme
(redline). i
just want to do that for DCE. any help is highly
appreciated.
Xmgrace.
-Justin
Regards
Vinoth
On Wed, Oct 20, 2010 at 5:33 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:
vinothkumar mohanakrishnan wrote:
Hi Justin
I corrected the mistake what you said and i am
able to run
energy minimisation and equilibration. but when i
view my
em.gro
and equilibration.gro in VMD it seems to me that
the bonds
between the atoms are broken in molecules.I used
g_energy to
check weather the system has
VMD tries to guess where bonds should be, but does not
always
do a
good job. Your topology defines bonds. These are the
only bonds
that there will be. None can be broken or formed in
standard MD.
equilibrated to the required temperature (300K) i
found
that the
variation in the temperature was 100K (plus r
minus) . i
am not
able find out what went wrong. any help is highly
appreciated.
Without seeing your .mdp file, there's no way to know.
The
fluctuation does seem too high, though, unless your system
really is
just that unstable. Are other properties converged -
potential
energy, density, etc? What type of ensemble are you
using?
-Justin
Regards
Vinoth
On Mon, Oct 18, 2010 at 6:09 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>>>
<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 <mailto:jalem...@vt.edu>>>>> wrote:
vinothkumar mohanakrishnan wrote:
Dear Justin
what corrections i should make to
ffoplsaan.itp to
make it
correct. what i should give instead of CAB
and CLAA?.
You must use atom types, not names.
Unfortunately, you've
chosen to
use atom names, which are also types, which
makes all
of this
quite
confusing if you're not sure what you're doing.
You defined two new atom types - opls_966 (CAB) and
opls_967
(CLAA),
which are the only indicators you are allowed
to use if
introducing
new types. Thus, references to atom names
(CAC, CLAD)
will
generate
fatal errors.
i copied the .rtp .atp .itp files from
usr/local/gromacs/share/gromacs/top to my
working
directory and
added these parameters to the corresponding
files.
what
you mean
is should i need to add these parameters to
the source
directory
( usr/local/gromacs/share/gromacs/top)?
Your topology needs to be consistent with whatever
files need
to be
included. By default, Gromacs checks the working
directory first,
but if you've moved to a new (sub)directory to
carry
out further
steps, the grompp will not find your modified
files,
but will
instead locate only the default force field
files in
$GMXLIB.
Either keep all your work in one directory
(which can get
messy),
or make use of the "include" keyword in the
.mdp file.
Any
directory specified there will be searched
after the
working
directory, but before $GMXLIB.
-Justin
Regards
Vinoth
On Mon, Oct 18, 2010 at 5:27 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>>>
<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 <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>
<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 <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>>> wrote:
vinothkumar mohanakrishnan wrote:
Hi all
i added new atomtype for dichloroethane
(DCE) and
added the
corresponding parameters in the
.rtp, .atp,
.bon.itp, .nb.itp
respectively. given below are my
additions
to the
corresponding
files respectively.
*ffoplsaa.rtp*
[ DCE ]
[ atoms ]
CLAA opls_967 -0.2270 1
CAB opls_966 0.2270 1
CAC opls_966 0.2270 2
CLAD opls_967 -0.2270 2
[ bonds ]
CLAA CAB
CAB CAC
CAC CLAD
[ angles ]
CLAA CAB CAC
CAB CAC CLAD
[ dihedrals ]
CLAA CAB CAC CLAD
*ffoplsaa.atp*
opls_966 14.02700 ; CH2 for DCE
opls_967 35.45300 ; CL for DCE
*ffoplsaabon.itp*
[bondtypes]
CLAA CAB 1 0.17870
194137.6 ;
CL-CH2
for DCE
CAB CAC 1 0.15300
259408.0 ;
CH2-CH2
for DCE
CAC CLAD 1 0.17870
194137.6 ;
CL-CH2
for DCE
[angletypes]
CLAA CAB CAC 1 108.200
368.192 ;
C-C-CL
for DCE
CAB CAC CLAD 1 108.200
368.192 ;
C-C-CL
for DCE
[dihedraltypes]
CLAA CAB CAC CLAD 3
20.76096
-0.4184 27.011904 0.00000
0.00000 0.00000
; for DCE
You shouldn't be using atom names in the
[*types]
directives.
What
you should be using are the interpolated
types from
ffoplsaanb.itp,
thus you have only utilized opls_966
(CAB) and
opls_967 (CLAA).
*ffoplsaanb.itp*
opls_966 CAB 6 14.02700
0.227 A 3.98000e-01
4.76976e-01 ; CH2 of DCE
opls_967 CLAA 17 35.45300
-0.227 A 3.16000e-01
0.20920e+01 ; Cl of DCE
*dce.pdb*
HETATM 1 CLAA DCE 1 6.300
-2.280 1.360 1.00
20.00 CL
HETATM 2 CAB DCE 1 5.060
-3.540 1.500 1.00
20.00 C
HETATM 3 CAC DCE 1 4.320
-3.740 0.170 1.00
20.00 C
HETATM 4 CLAD DCE 1
3.270 -2.350
-0.210 1.00
20.00 CL
After adding all this, when i run
grompp i
get the
error as
*fatal error Unknown bond_atomtype
CLAA*.
can any
one tell me
why this happens?.
Have you been sure to #include the correct
(modified)
force field
files? That is, if you made a local
copy and
adjusted
them,
these
won't be the files that pdb2gmx will
#include
by default.
-Justin
Regards
Vinoth
--
========================================
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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-- ========================================
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> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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Virginia Tech
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Virginia Tech
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