[gmx-users] Re:gmx-users Digest, Vol 113, Issue 54

Dear prof. after i calculating the secondary strucure of residues frome 20 to 60 using do_dssp . And then i use xpm2ps to show the picture with ps.m2p, but the residue order number of y-axis start form 1 not the 20. how can i change the order of residue? Thank you very much! At

[gmx-users] SD integrator

Hi all, I have been posting for a while with my problems in simulating peptides inside CNTs. After a lot of trials it seems like simulating the CNT with bonds and angles seems like a wise thing to do. I am using the SD integrator + PR barostat. It seems like improper thermostatting can blow up

Fwd: [gmx-users] SD integrator

There must be some problem with degrees of freedom in your system... Dr. Vitaly V. Chaban -- Forwarded message -- From: HANNIBAL LECTER hanniballecte...@gmail.com Date: Fri, Sep 13, 2013 at 7:15 PM Subject: [gmx-users] SD integrator To: Discussion list for GROMACS users

Re: [gmx-users] Re: Gromacs: GPU detection

FYI, I've file a bug report which you can track if interested: http://redmine.gromacs.org/issues/1334 -- Szilárd On Sun, Sep 1, 2013 at 9:49 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: I may have just come across this issue as well. I have no time to investigate, but my guess is that it's

[gmx-users] MD simulations of Tyrosinase using GROMACS

Dear GMX users, I am trying to carry out MD simulations with tyrosinase protein. Tyrosinase is a tyoe-3 copper protein. In its oxygen binding active site, the protein has two copper atoms that bind to two oxygen atoms in a peroxo configuration. Each copper is co-ordinated by three histidine

Re: Fwd: [gmx-users] SD integrator

Do you couple CNT as a separate T-group? It should be done so. I think your systems blows up because of incorrectly defined bonded parameters for the tube, not due to thermostatting. For instance, you might not define all the valence angles and dihedrals. See my papers for the parameters for

[gmx-users] Distance calculation

Hi , I there any tool to calculate distance between particular atom from one group(protein) to particular atom from another group(DMPC lipid in Bilayer). For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in DMPC lipid. Thanks Rama -- View this message in context:

Re: [gmx-users] how to make a index file

Please don't reply to the entire digest. On 9/13/13 9:25 AM, aixintiankong wrote: Dear prof. after i calculating the secondary strucure of residues frome 20 to 60 using do_dssp . And then i use xpm2ps to show the picture with ps.m2p, but the residue order number of y-axis start