[gmx-users] Bond paths

Hi everyone, this is a general question please does anyone know what bond paths means, and what it has to do with dihedrals? Thank you Carla ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] Bond paths

Carla Jamous wrote: Hi everyone, this is a general question please does anyone know what bond paths means, and what it has to do with dihedrals? http://www.google.com.au/search?q=bond+paths, and not much it seems. Mark ___ gmx-users mailing list

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, As per the suggestions, I have run NPT equillibration (without constraints) for 1ns and observed the average values and plots in the xmgrace as follows: 1) Pressure Energy Average RMSD Fluct. Drift Tot-Drift

Re: [gmx-users] Error during NVT equillibration with nvt.log file

ram bio wrote: Dear Justin, As per the suggestions, I have run NPT equillibration (without constraints) for 1ns and observed the average values and plots in the xmgrace as follows: 1) Pressure Energy Average RMSD Fluct. Drift Tot-Drift

Re: [gmx-users] how to stop duplicate atoms from being deleted

Hi Justin, Thanks for the new suggestion. However, wouldn't this again involve the sorting of my .pdb file? I have modified the specbond.dat 3 MSI SI4 MOO 2 0.16 MCM MCM MSI SI4 MOH OH2 0.16 MCM MCM MOH OH2 MHH 1 0.101 MCM

Re: [gmx-users] Which membrane result is more reliable?

Hi Justin, Sorry I forgot the attachment. Can you see if these files are ok in terms of sequences and more or less accurately represent both DMPC and DMPE? they were built in Teilman lab I believe DMPE: http://sites.google.com/site/kbessonov/dmpe.itp?attredirects=0d=1 DMPC:

[gmx-users] Re: Which membrane result is more reliable?

Sorry I've just noted that once of the messages made it to the forum, sorry for repetition. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

[gmx-users] CG Mapping section for g_fg2cg

Dear all, how can I create the mapping section for g_fg2cg in the atomistic *.itp file? The handout from the Coarse Graining Workshop 2009 says that pdb2gmx has this ability but I can't find it: http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/CGWS_Tutorial.pdf/download. By

Re: [gmx-users] how to stop duplicate atoms from being deleted

Jennifer Williams wrote: Hi Justin, Thanks for the new suggestion. However, wouldn't this again involve the sorting of my .pdb file? I have modified the specbond.dat 3 MSI SI4 MOO 2 0.16 MCM MCM MSI SI4 MOH OH2 0.16 MCM MCM MOH OH2

Re: [gmx-users] CG Mapping section for g_fg2cg

It is not clear what you actually want to do! 1- You want to generate a topology for MARTINI: follow the tutorial, which I believe is clear. 2- you want to play with the reverse transformation. For a protein I believe that there is a parameter file that contains the CG-AA mapping. For other

Re: [gmx-users] Which membrane result is more reliable?

Kirill Bessonov wrote: Hi Justin, Sorry I forgot the attachment. Can you see if these files are ok in terms of sequences and more or less accurately represent both DMPC and DMPE? they were built in Teilman lab I believe DMPE:

Re: [gmx-users] CG Mapping section for g_fg2cg

Dear Xavier, well, sorry. I was on the wrong way. :-) I'm trying to map a model from the atomistic scale into CG. All the time I searched for a possibility to define atoms to CG-Beads. I was confused because of the awk script atom2cg which simply puts out only a couple of atom types that were not

[gmx-users] Re: Creating topology for a small organic molecule

Dear Gunnar, I am right now on holidays but in 2 weeks I can help you with antechamber unix problems you may be facing. For the moment I suggest you to read acpypi and antechamber documentation with attention, practice the tutorials and examples. I understand that many users urge to use such

[gmx-users] Parameters for neutral phosho-amino acids

Hi everyone.  I'm doing some simulations of a phosphorylated peptide.  Right now, I'm using the amber force field with some parameters that were obtained for charged phosphorylated amino acids in a paper I found.  Now I want to simulate uncharged phosphate groups, but the paper only gave

Re: [gmx-users] Parameters for neutral phosho-amino acids

Michael McGovern wrote: Hi everyone. I'm doing some simulations of a phosphorylated peptide. Right now, I'm using the amber force field with some parameters that were obtained for charged phosphorylated amino acids in a paper I found. Now I want to simulate uncharged phosphate groups, but

[gmx-users] Square-Well-Potential

Dear all, I searched the mailing-lists and I wonder if there were any attempts to approximate discontinuous interaction potentials like square-well with the tabulated potential function? Best Regards, Bob ___ gmx-users mailing list

[gmx-users] Energy Minimization of DNA

Hello all, how are you doing today? I've been trying to get a stable DNA MD simulation to work for me, but I think my problem lies in an insufficiently energy minimized system prior to running the pr step. I'm using the ffamber99 force field and I've successfully simulated many ns of MD using