Hi Justin<br><br>Below is my nvt.mdp (nvt equilibration) file.i think probably you can have look at it and its not such big.<br><br>define = -DFLEXIBLE <br>integrator = md <br>
nsteps = 50000 <br>dt = 0.002 <br>nstxout = 100 <br>nstvout = 100 <br>nstenergy = 100 <br>
nstlog = 100 <br>constraint_algorithm = shake <br>constraints = none <br>unconstrained_start = yes <br>shake_tol = 0.0001 <br>morse = no <br>
ns_type = grid <br>nstlist = 5 <br>rlist = 1.0 <br>coulombtype = PME <br>rcoulomb = 1.0 <br>
vdwtype = Cut-off <br>rvdw = 1.0 <br>pme_order = 4 <br>fourierspacing = 0.16 <br>pbc = xyz <br>
tcoupl = V-rescale <br>tc-grps = system <br>tau_t = 0.1 <br>ref_t = 300 <br>DispCorr = Ener <br>
gen_vel = yes <br>gen_temp = 300 <br>gen_seed = 173529 <br><br>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.<br>
<br>Regards<br>Vinoth<br><br><div class="gmail_quote">On Thu, Oct 21, 2010 at 4:56 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 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>
</blockquote>
<br></div>
This is impossible to assess without seeing your .mdp settings. A fluctuation of 10% is probably fine.<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;">
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>
</blockquote>
<br></div>
Xmgrace.<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 class="im"><br>
<br>
On Wed, Oct 20, 2010 at 5:33 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></div><div class="im">
Hi Justin<br>
<br>
I corrected the mistake what you said and i am able to run<br>
energy minimisation and equilibration. but when i view my em.gro<br>
and equilibration.gro in VMD it seems to me that the bonds<br>
between the atoms are broken in molecules.I used g_energy to<br>
check weather the system has<br>
<br>
<br>
VMD tries to guess where bonds should be, but does not always do a<br>
good job. Your topology defines bonds. These are the only bonds<br>
that there will be. None can be broken or formed in standard MD.<br>
<br>
<br>
equilibrated to the required temperature (300K) i found that the<br>
variation in the temperature was 100K (plus r minus) . i am not<br>
able find out what went wrong. any help is highly appreciated.<br>
<br>
<br>
Without seeing your .mdp file, there's no way to know. The<br>
fluctuation does seem too high, though, unless your system really is<br>
just that unstable. Are other properties converged - potential<br>
energy, density, etc? What type of ensemble are you using?<br>
<br>
-Justin<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
On Mon, Oct 18, 2010 at 6:09 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 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>
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<br>
chosen to<br>
use atom names, which are also types, which makes all of this<br>
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<br>
(CLAA),<br>
which are the only indicators you are allowed to use if<br>
introducing<br>
new types. Thus, references to atom names (CAC, CLAD) will<br>
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<br>
directory and<br>
added these parameters to the corresponding files. what<br>
you mean<br>
is should i need to add these parameters to the source<br>
directory<br>
( usr/local/gromacs/share/gromacs/top)?<br>
<br>
<br>
Your topology needs to be consistent with whatever files need<br>
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<br>
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>
<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>>><br>
<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>><br>
<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<br>
added the<br>
corresponding parameters in the .rtp, .atp,<br>
.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<br>
for DCE<br>
CAB CAC 1 0.15300 259408.0 ; CH2-CH2<br>
for DCE<br>
CAC CLAD 1 0.17870 194137.6 ; CL-CH2<br>
for DCE<br>
<br>
[angletypes]<br>
CLAA CAB CAC 1 108.200 368.192 ;<br>
C-C-CL<br>
for DCE<br>
CAB CAC CLAD 1 108.200 368.192 ;<br>
C-C-CL<br>
for DCE<br>
<br>
[dihedraltypes]<br>
CLAA CAB CAC CLAD 3 20.76096<br>
-0.4184 27.011904 0.00000 0.00000 0.00000<br>
; for DCE<br>
<br>
<br>
You shouldn't be using atom names in the [*types]<br>
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<br>
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<br>
-0.210 1.00<br>
20.00 CL<br>
<br>
After adding all this, when i run grompp i get the<br>
error as<br>
*fatal error Unknown bond_atomtype CLAA*. can any<br>
one tell me<br>
why this happens?.<br>
<br>
<br>
Have you been sure to #include the correct (modified)<br>
force field<br>
files? That is, if you made a local copy and adjusted<br>
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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>><br>
<<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
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<br>
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-- ========================================<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
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Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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========================================<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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