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 -CH2- and -CH= will have two connections each. and the distances with other united carbons are 0.154nm and 0.140 nm as I have mentioned before. I have been giving the same information in the .n2t file. Based on the order in which they appear in the .n2t file, the atom appearing first is being taken by x2top to create the topology. I hope I made my problem clear. I'm unable to post my .n2t file now as I do not have it with me at the moment. If required I can post it tomorrow. Thanks and Regards Sridhar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 gromos or opls ua ? Thanks and Regards Sridhar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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. This may be due to the small difference in distance (0.140 nm and 0.154 nm). Can anyone suggest a way to go about this? Thanks and Regards Sridhar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx x2top, VERSION 5.0.2 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx x2top -f polyngta_nm.pdb -ff poly -o check.rtp -v -param Opening force field file ./poly.ff/atomname2type.n2t There are 9 name to type translations in file ./poly.ff Generating bonds from distances... atom 162 There are 7 different atom types in your sample Generating angles and dihedrals from bonds... Segmentation fault (core dumped) It returned an error. I have seen posts earlier regarding an error in the code in version 5. Is it related to that? Also in many posts I have seen that even if it generates topology, the generated topology must be carefully checked. Is it system dependent? Thank You Sridhar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 them using glutaraldehyde and obtained coordinate file (from Materials Studio) for the same. Currently I am trying to create rtp entries, to create topology using pdb2gmx. As the polymer chains are cross linked, I am trying to use special bonds file. For this I am defining the cross link structures between the two polymer chains as a separate residue and am trying to add the bonds between the polymer chains and cross linkers as special bonds (As I understood from the manual). It would be really helpful for me to if anyone can share their thoughts/experience on creating topology for crosslinked polymer networks. Is the approach mentioned above correct? Is there any better way to generate topology for such systems ? Thank You Sridhar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
