[gmx-users] building long polymer chain

[Moeed]

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.

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)

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?

  *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,
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100608/546633f5/attachment.html>