Hi justin<br><br>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?<br>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.<br>
<br>Regards<br>Vinoth<br><br><div class="gmail_quote">On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Justin<br>
<br>
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 <br>
</blockquote>
<br></div>
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.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
<br>
</blockquote>
<br></div>
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?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Regards<br>
Vinoth<div><div></div><div class="h5"><br>
<br>
On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<br>
Dear Justin<br>
<br>
what corrections i should make to ffoplsaan.itp to make it<br>
correct. what i should give instead of CAB and CLAA?.<br>
<br>
<br>
You must use atom types, not names. Unfortunately, you've chosen to<br>
use atom names, which are also types, which makes all of this quite<br>
confusing if you're not sure what you're doing.<br>
<br>
You defined two new atom types - opls_966 (CAB) and opls_967 (CLAA),<br>
which are the only indicators you are allowed to use if introducing<br>
new types. Thus, references to atom names (CAC, CLAD) will generate<br>
fatal errors.<br>
<br>
<br>
i copied the .rtp .atp .itp files from<br>
usr/local/gromacs/share/gromacs/top to my working directory and<br>
added these parameters to the corresponding files. what you mean<br>
is should i need to add these parameters to the source directory<br>
( usr/local/gromacs/share/gromacs/top)?<br>
<br>
<br>
Your topology needs to be consistent with whatever files need to be<br>
included. By default, Gromacs checks the working directory first,<br>
but if you've moved to a new (sub)directory to carry out further<br>
steps, the grompp will not find your modified files, but will<br>
instead locate only the default force field files in $GMXLIB.<br>
Either keep all your work in one directory (which can get messy),<br>
or make use of the "include" keyword in the .mdp file. Any<br>
directory specified there will be searched after the working<br>
directory, but before $GMXLIB.<br>
<br>
-Justin<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<br>
Hi all<br>
<br>
i added new atomtype for dichloroethane (DCE) and added the<br>
corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp<br>
respectively. given below are my additions to the<br>
corresponding<br>
files respectively.<br>
<br>
*ffoplsaa.rtp*<br>
<br>
[ DCE ]<br>
[ atoms ]<br>
CLAA opls_967 -0.2270 1<br>
CAB opls_966 0.2270 1<br>
CAC opls_966 0.2270 2<br>
CLAD opls_967 -0.2270 2<br>
<br>
[ bonds ]<br>
CLAA CAB<br>
CAB CAC<br>
CAC CLAD<br>
<br>
[ angles ]<br>
CLAA CAB CAC<br>
CAB CAC CLAD<br>
<br>
[ dihedrals ]<br>
CLAA CAB CAC CLAD<br>
<br>
*ffoplsaa.atp*<br>
<br>
opls_966 14.02700 ; CH2 for DCE<br>
opls_967 35.45300 ; CL for DCE<br>
<br>
*ffoplsaabon.itp*<br>
<br>
[bondtypes]<br>
CLAA CAB 1 0.17870 194137.6 ; CL-CH2 for DCE<br>
CAB CAC 1 0.15300 259408.0 ; CH2-CH2 for DCE<br>
CAC CLAD 1 0.17870 194137.6 ; CL-CH2 for DCE<br>
<br>
[angletypes]<br>
CLAA CAB CAC 1 108.200 368.192 ; C-C-CL<br>
for DCE<br>
CAB CAC CLAD 1 108.200 368.192 ; C-C-CL<br>
for DCE<br>
<br>
[dihedraltypes]<br>
CLAA CAB CAC CLAD 3 20.76096 -0.4184 27.011904 0.00000 0.00000 0.00000 ; for DCE<br>
<br>
<br>
You shouldn't be using atom names in the [*types] directives.<br>
What<br>
you should be using are the interpolated types from<br>
ffoplsaanb.itp,<br>
thus you have only utilized opls_966 (CAB) and opls_967 (CLAA).<br>
<br>
*ffoplsaanb.itp*<br>
<br>
<br>
opls_966 CAB 6 14.02700 0.227 A 3.98000e-01<br>
4.76976e-01 ; CH2 of DCE<br>
opls_967 CLAA 17 35.45300 -0.227 A 3.16000e-01<br>
0.20920e+01 ; Cl of DCE<br>
<br>
*dce.pdb*<br>
<br>
HETATM 1 CLAA DCE 1 6.300 -2.280 1.360 1.00<br>
20.00 CL<br>
HETATM 2 CAB DCE 1 5.060 -3.540 1.500 1.00<br>
20.00 C<br>
HETATM 3 CAC DCE 1 4.320 -3.740 0.170 1.00<br>
20.00 C<br>
HETATM 4 CLAD DCE 1 3.270 -2.350 -0.210 1.00<br>
20.00 CL<br>
<br>
After adding all this, when i run grompp i get the error as<br>
*fatal error Unknown bond_atomtype CLAA*. can any one tell me<br>
why this happens?.<br>
<br>
<br>
Have you been sure to #include the correct (modified) force field<br>
files? That is, if you made a local copy and adjusted them,<br>
these<br>
won't be the files that pdb2gmx will #include by default.<br>
<br>
-Justin<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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