[gmx-users] building long polymer chain

[Justin A. Lemkul]

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,
> 

-- 
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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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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