Moeed wrote:
Hello Justin,
I am trying to generate the top file for polyethylene chain using the
information from the archive:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html. In
the former post you said parameters in the I am referring to are not
necessarily correct.
1- By parameters you mean the coordinates in pdb file? The residues in
this link seem correct to me but I am not sure if the hdb file is correct.
The term "parameters" refers to atom types and charges. The example I created
for the post above is based on what I believed to be plausible atom types and
charges for alkyl groups, but I have never validated these items for use in
polymers. The post was to be instructive only. Maybe the parameters are
suitable, maybe they are not.
2- Could you please tell me how to generate a longer chain with the
given residue types proposed in the above post.
ATOM 1 C1 EthB 1 1.000 1.540 0.000
ATOM 2 C2 EthB 1 2.456 2.041 0.000
ATOM 3 C1 Eth 2 2.456 3.581 0.000
ATOM 4 C2 Eth 2 3.912 4.083 0.000
ATOM 5 C1 EthE 3 3.912 5.623 0.000
ATOM 6 C2 EthE 3 5.368 6.124 0.000
END
Here I do not see hydrogen atoms. I have created a long chain with 100
monomer units using Ascalaph designer. However the file is not properly
formatted. i.e atoms are not numbered and residue name is missing. I do
not want to alter the file by hand. Can you guide me how I can build a
long chain with the residues you proposed in the above post (including
hydrogen atoms)
The residues I created assume that there are corresponding entries in the
appropriate .hdb file, which I provided in the post you quote. As for creating
a coordinate file:
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
HETATM 1 C 1 2.739 2.554 -0.012
-0.390 C
HETATM 2 H 1 2.736 3.644 -0.012
0.130 H
HETATM 3 H 1 2.190 2.217 -0.893
0.130 H
HETATM 4 H 1 2.190 2.217 0.868
0.130 H
HETATM 5 C 2 4.155 1.993 -0.012
-0.260 C
.
.
HETATM 291 H 97 72.086 -97.891 -0.012
0.130 H
HETATM 292 H 97 70.558 -97.880 0.869
0.130 H
HETATM 293 H 97 70.558 -97.880 -0.893
0.130 H
3- I have also an inquiry about the density of my solvent. One of the
experts told me:
Best thing you can do is, make a NPT simulation (look for the right
compresibility) and look how much your density is off,if it's only a
little your fine.
I dont realize the statement "look how much your density is off"?
The desnity is approx. 71000 Kg/m3 (4molecuels per nm3). From NPT run I
see the density is 577 Kg/m3. and the volume is
30 nm3 (values from g_energy). How can I make sure if density changes
are reasonable?
You need experimentally-derived densities to compare your values. To what does
71000 kg/m^3 correspond? If that's your target value, you're nowhere close.
For polyethylene, the density depends on the molecular weight and geometry,
correct? The target value should depend upon what you're trying to model.
-Justin
*Volume * 30.9568* 0.374111 0.204815
Density (SI) *577.914* 6.97804 3.80252
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 297.366 12.086 11.4021 1.38812
13.884
Pressure (bar) -30.0299 746.524 745.665 -12.3992
-124.017
*Volume 30.9568 0.374111 0.204815 -0.108427
-1.08449*
**
*Density (SI) 577.914 6.97804 3.80252 2.02643
20.2684*
pV -55.9879 1393.39 1391.81 -22.9985
-230.031
#Surf*SurfTen 218.21 4871.45 4871.37 -9.30662
-93.0848
T-HEX 297.366 12.086 11.4021 1.38812
13.884
Lamb-HEX 1.00011 0.000588089 0.000561362 -6.07045e-05
-0.000607166
Heat Capacity Cv: 12.5027 J/mol K (factor = 0.0016519)
Isothermal Compressibility: 0.00011012 /bar
Adiabatic bulk modulus: 9080.99 bar
with mdp file:
> ; Pressure coupling: Pressure coupling is not on
> Pcoupl = berendsen
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
Thanks,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
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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