[gmx-users] calcium diffuses away from the protein during MD

Dear Users, I performed MD simulation on a calcium binding protein with bound calcium starting from the crystal structure using gromos96 forcefield with explicit solvent with NVT ensembles. I performed energy minimization of calcium bound protein with water and following this position restraint m

[gmx-users] generation of acetic acid protonated .itp file

GROMOS96 forcefield. Your help will be appreciated. Best regards, Dr. Sunita Patel - Visiting Fellow Department of Chemical Sciences T.I.F.R., Homi Bhabha Road, Colaba Mumbai - 45 - -- gmx-users mailing

[gmx-users] do_dssp failed to execute

Dear User, I set the path for dssp executable in .bashrc file. Still getting following error. Could anybody suggest what would be the problem. error message Select a group: 5 Selected 5: 'MainChain' There are 134 residues in your selected group Opening lib

Re: [gmx-users] do_dssp failed to execute

Dear Mark, On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote > - Original Message - > From: Sunita Patel > Date: Monday, October 11, 2010 22:50 > Subject: [gmx-users] do_dssp  failed to execute > To: Discussion list for GROMACS users > > > Dear User, >

[gmx-users] disparity in RMSD calculation

Dear Users, I calculated RMSD for a trajectory with same reference structure using GROMACS and VMD. I observed completely difference plots for the same data. Please see the attached file. What could be the cause for this disparity? Thanks for any suggestion. Sunita <>-- gmx-users mailing lis

Re: [gmx-users] disparity in RMSD calculation

On Sat, 20 Nov 2010 01:13:51 -0500, Yongchul Chung wrote > On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel > wrote: > Dear Users, > > I calculated RMSD for a trajectory with same reference structure using GROMACS > and VMD. I observed completely difference plots for the sam

RE: [gmx-users] disparity in RMSD calculation

mark.abra...@anu.edu.au > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] disparity in RMSD calculation > > > > On 20/11/2010 4:54 PM, Sunita Patel wrote: > > > Dear Users, > > > > > > I calculated RMSD for a trajectory with same reference s

Re: [gmx-users] disparity in RMSD calculation

On Sat, 20 Nov 2010 19:05:35 +1100, Mark Abraham wrote > On 20/11/2010 4:54 PM, Sunita Patel wrote: > > Dear Users, > > > > I calculated RMSD for a trajectory with same reference structure using > > GROMACS > > and VMD. I observed completely difference plots f