Re: [gmx-users] building up a long polymer chain

Moeed wrote: Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.0

[gmx-users] building up a long polymer chain

Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.050 -4.790 0.326

Re: [gmx-users] building up a long polymer chain

Moeed wrote: Hello Justin, As you pointed out at the end of former message my real problem is generation of a properly formatted structure file for PE. Within last few weeks I tried to obtain the structure file using that known link... but that was not helpful to me since those residues ne

[gmx-users] building up a long polymer chain

Hello Justin, As you pointed out at the end of former message my real problem is generation of a properly formatted structure file for PE. Within last few weeks I tried to obtain the structure file using that known link... but that was not helpful to me since those residues need atom numbering..Hd

Re: [gmx-users] building up a long polymer chain

Moeed wrote: for PE. or maybe this dies not affect the results since charges and mass are the same..?! You can set the charges to whatever you want them to be, so this is no issue at all. Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the suitable atom type for car

[gmx-users] building up a long polymer chain

Dear experts, For hexane molecule I used atom types opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols opls_158 12.01100 ; all-atom C: CH, alcohols in residue file: [ HEX ] [ atoms ] C1 opls_157-0.180 1 H11 opls_140 0.060 1 H12 opls_140 0.060 1