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>> 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>>> 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>>>> 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
-- ========================================
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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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> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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