Re: [gmx-users] Index file

2012-12-30 Thread Chandan Choudhury
On Mon, Dec 31, 2012 at 1:07 PM, Chandan Choudhury wrote: > > > > On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > >> Dear all, >> I had a .pdb file containing protein, popc, and ions. So I used editconf >> to make a .gro file. But when I want to make an in

Re: [gmx-users] Index file

2012-12-30 Thread Chandan Choudhury
On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh wrote: > Dear all, > I had a .pdb file containing protein, popc, and ions. So I used editconf > to make a .gro file. But when I want to make an index file, 2 CL ions are > not identified, so I can not choose it. > > use make_ndx f .pdb > Sincerely

[gmx-users] Index file

2012-12-30 Thread Shima Arasteh
Dear all, I had a .pdb file containing protein, popc, and ions. So I used editconf to make a .gro file. But when I want to make an index file, 2 CL ions are not identified, so I can not choose it. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

RE: [gmx-users] PMF Transmembrane proteins

2012-12-30 Thread Nash, Anthony
Hi Justin, Thanks for the help. The block analysis has done wonders! I had been interested in seeing how the PMF graphs converged, i.e., 0-1ns, 0-2ns, 0-3ns. Of course this always includes the earliest time steps. Long story short, by cutting off the first 10ns so I am only sampling 10ns-40ns,

Re: [gmx-users] PMF Transmembrane proteins

2012-12-30 Thread Justin Lemkul
On 12/30/12 2:57 PM, Nash, Anthony wrote: Dear Justin Thanks for your reply. I am studying a TM peptide, looking at how favourable the front and reverse face are. Hence, different orientations but the same composition of amino acids. I then have a duplicate of this system (call it system B),

RE: [gmx-users] PMF Transmembrane proteins

2012-12-30 Thread Nash, Anthony
Dear Justin Thanks for your reply. I am studying a TM peptide, looking at how favourable the front and reverse face are. Hence, different orientations but the same composition of amino acids. I then have a duplicate of this system (call it system B), but with a couple of residue substitution

Re: [gmx-users] PMF Transmembrane proteins

2012-12-30 Thread Justin Lemkul
On 12/30/12 12:28 PM, Nash, Anthony wrote: Dear gmx users, I posted a couple of weeks ago with regards to correctly using umbrella sampling and the WHAM on atomistic transmembrane proteins with a reaction coordinate as a function of interhelical distance. I have a single TM dimer, but with a d

[gmx-users] PMF Transmembrane proteins

2012-12-30 Thread Nash, Anthony
Dear gmx users, I posted a couple of weeks ago with regards to correctly using umbrella sampling and the WHAM on atomistic transmembrane proteins with a reaction coordinate as a function of interhelical distance. I have a single TM dimer, but with a different transmembrane domain face at the he

Re: [gmx-users] water can not be settled

2012-12-30 Thread Justin Lemkul
On 12/30/12 6:25 AM, Shima Arasteh wrote: Hi, If I get a fatal error of " water molecule can not be settled", where in log file or bash I can find the disturbing water molecules? Would you please guide me? I constantly get this fatal error! :-( http://www.gromacs.org/Documentation/Errors#

[gmx-users] water can not be settled

2012-12-30 Thread Shima Arasteh
Hi, If I get a fatal error of " water molecule can not be settled", where in log file or bash I can find the disturbing water molecules? Would you please guide me? I constantly get this fatal error! :-( Thanks in advance. Sincerely, Shima  -- gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] water can not be settled

2012-12-30 Thread Shima Arasteh
Hi, If I get a fatal error of " water molecule can not be settled", where in log file or bash I can find the disturbing water molecules? Would you please guide me? I constantly get this fatal error! :-( Thanks in advance.   Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org h

Re: [gmx-users] Re: Simulation of 2D lattice model

2012-12-30 Thread James Starlight
Hi Leandro! Actually I need such model of simple 2D lattice for study of the hessian matrix. So I'd like to perform simulation of very simple system without any rotation freedoms and calculate eigenvectors from that trajectory by means of Esential dynamics analysis. Than I'd like to watch on what