Re: [gmx-users] How does x2top recognize between alkane C and alkene C

Hi Dr. Justin Lemkul, Thank you for responding again. I'm still not understanding it :(. I'll try to be more clear. Taking the example of OPLS UA, we have different atom types for united alkene atoms (-CH= and CH2=) and alkanes (-CH2-). When I represent the connections in n2t file, the

[gmx-users] How does x2top recognize between alkane C and alkene C

Thank you for the response. In case of an all atom representation, the connections are different. What about a united atom representation? The g_x2top supports Gromacs 53a5 forcefield right? Can we get a topology with x2top only for an all atom representation? Or is there anyway to get it for

[gmx-users] How does x2top recognize between alkane C and alkene C

Dear gromac users, I'm using g_x2top (4.6.7 version), to generate a topology. The compound contains double bonds. I have a problem in setting correct topology. The C1 in both the cases -C1H=C2H2 and -C1H2- is being assigned the same type, though I'm mentioning different distances in the n2t file.

Re: [gmx-users] Topology for Cross linked polymer chains

Hi Justin Lemkul, Thank you very much for the reply. I have tried using x2top for generating topology. I copied contents of opls ff to poly ff and added some atoms and ran the command. The output was as follows: GROMACS is written by: Emile Apol Rossen Apostolov Herman

[gmx-users] Topology for Cross linked polymer chains

Dear Gromacs Users, I have started to use Gromacs recently to simulate certain properties of polymer hydrogels. I have taken Poly Vinyl Alcohol cross linked with Glutaraldehyde as my system. In this system, I have taken two long chains of polymers and cross linked