[gmx-users] construct the long polymer chain

Hi I have been following http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html(procedure by Justin) to construct the Polyethylene (PE). However, I can only get the PE with length 6 just like CH3-CH2-CH2-CH2-CH2-CH3. Therefore, I want to know how to obtain the long polymer chain(e.g. l

[gmx-users] Re: polymer duplicate atoms

I follow your advice to edit the bond conditions of residues Fbg and Fen in my rtp file. Subsequently, I should modify the hdb file to add hydrogens for Fbg and Fen. However, I get the fatal error message " Atom +C1 not found in residue Fbg 113, rtp entry Fbg while adding hydrogens." I can successf

[gmx-users] Re: polymer duplicate atoms

I have successfully construct the polymer chain of length 1 using the OPLS force field. The rtp file as follow: ; F2311 - this is an internal residue [ Fre ] [ atoms ] C1opls_135 -0.5681 H11 opls_1400.2741 H12 opls_1400.2731 C

[gmx-users] Re: polymer duplicate atoms

I want to construct a polymer chain of F2311 with 112 length. In my pdb file, residues Fre, Fbg and Fen denote the repeat unit —(CH2-CF2-CF2-CFCl)— ,terminate part (Fbg:the beginning of chain with methyl; Fen: the end of chain with methyl), respectively. It looks like CH3-A-B... A-B-A-B-A-B...-A-B

[gmx-users] Re: polymer duplicate atoms

I want to construct a polymer chain of F2311 with 112 length. In my pdb file, residues Fre, Fbg and Fen denote the repeat unit —(CH2-CF2-CF2-CFCl)— ,terminate part (Fbg:the beginning of chain with methyl; Fen: the end of chain with methyl), respectively. It looks like CH3-A-B... A-B-A-B-A-B...-A-B

[gmx-users] Re: polymer duplicate atoms

Dear Dallas Thanks for your reply. I followed the way of you said to modify the residue number in sequence. It generated a complete sturctural file (conf.gro) without deleting the duplicate atoms. However, it denoted another strange structure which contained many seperated residue —(CH2-C

[gmx-users] RE: polymer duplicate atoms

Dear Dallas Thanks for your reply. I followed the way of you said to modify the residue number in sequence. It generated a complete sturctural file (conf.gro) without deleting the duplicate atoms. However, it denoted another strange structure which contained many seperated residue —(CH2-CF

[gmx-users] polymer duplicate atoms

Hi I use the pdb2gmx to generate topology file of polymer f2311(fluororubber) with the incorrect information of GROMACS structural file (conf.gro). There are 680 atoms in my input (.pdb) file. But, 660 atoms are deleted in conf.gro file because of duplicate atoms. The printed message as follow: <