Re: [gmx-users] Problem with reading AMBER trajectories

2013-10-18 Thread Mark Abraham
Can this file be opened in VMD itself? Mark On Oct 18, 2013 6:21 AM, "anu chandra" wrote: > Dear Gromacs users, > > I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few > analysis. Unfortunately I ended-up with the following error. > > #

Re: [gmx-users] Bilayer thickness error

2013-10-18 Thread Justin Lemkul
On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote: Hi, This is my input file for calculating bilayer thickness in absence of peptide: ## Input file and input file parameters coord_file md.gro file_type gro num_frames 1 num_lipid_types1 res

Re: [gmx-users] Problem with reading AMBER trajectories

2013-10-18 Thread anu chandra
Hi Mark, Yes. I do can able to load the trajectories successfully in VMD with the file format option of ' AMBER coordinate with periodic box'. I am using VMD 1.9 version. Regards Anu On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham wrote: > Can this file be opened in VMD itself? > > Mark > On O

Re: [gmx-users] Bilayer thickness error

2013-10-18 Thread Archana Sonawani-Jagtap
thank you so much. It was such a stupid error from my side. On Fri, Oct 18, 2013 at 5:08 PM, Justin Lemkul wrote: > > > On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote: > >> Hi, >> This is my input file for calculating bilayer thickness in absence of >> peptide: >> ## Input file and inpu

Re: [gmx-users] Problem with reading AMBER trajectories

2013-10-18 Thread Mark Abraham
OK. All GROMACS does is feed your filename extension to the VMD library and let it choose how to read the file based on that. If that doesn't make sense (and it seems it doesn't, because GROMACS wasn't told about the number of atoms, and it needs to know), then the ball is back to you to choose the

[gmx-users] modification of LJ potential

2013-10-18 Thread Zuzana Benkova
Dear GROMACS users,I went through the mailing list but I am still not sure about my problem. I am going to simulate two chains in a tube using GROMACS. The chains are modeled as strings of connected beads and I would like to describe the interaction with the tube aligned with z axis and passing thr

[gmx-users] Molecular dynamics with LEGO?

2013-10-18 Thread Tsjerk Wassenaar
Hi :) Apologies if this seems inappropriate, but I would like to ask as many people as I can to give support for the molecular modeling LEGO project at http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will consider producing the bricks required for such models, and we can add cool

Re: [gmx-users] Molecular dynamics with LEGO?

2013-10-18 Thread jkrieger
Hi Tsjerk, In my opinion, we don't need to develop LEGO specifically for this - something already exists, which I played with in school. The molymod pieces (http://www.molymod.com/) already include bendy pieces, which are the next step on the lego website you advertise. Best wishes James > Hi :)

Re: [gmx-users] Molecular dynamics with LEGO?

2013-10-18 Thread Tsjerk Wassenaar
Hi James, There are models, yes. But if a manufacturer like LEGO is taking this up, it can make the models much cheaper and more easily available. In addition, the LEGO models would allow more flexibility in building and handling. And you can combine it with your other LEGO ;) And, yes, bendy pie