[gmx-users] Error Esitmation of replicates

Dear all, We have run of three temperatures simulation (unfolding) and three replicates of them. we are interested to calculate the experimental errors. anyone has idea how do it? regards, Ravi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] FW: protein split over boundary

Hello anahita, use pbc in your simulation. regards, Ravi   --- On Fri, 1/4/11, anahita wrote: From: anahita Subject: [gmx-users] FW: protein split over boundary To: "'Discussion list for GROMACS users'" Date: Friday, 1 April, 2

Re: [gmx-users] POPC Membrane + protein dynamics

eerut   --- On Sat, 27/3/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] POPC Membrane + protein dynamics To: "Gromacs Users' List" Date: Saturday, 27 March, 2010, 4:59 PM ravi sharma wrote: > > Dear, > This is

Re: [gmx-users] POPC Membrane + protein dynamics

Dear, This is the case when you added some ions in your pdb but not define it in your topology, Go in the end of you topology and subtract the number of molecule added. Also define the number of ions added and the name of the ion. like : NA 14 regards, Ravi   

Re: [gmx-users] protein running out of box

Dear Zhen Chen Protein is located stranger(sometime at the one side of the protein,in other frame other  side). Its not a problem.  Your simulation is fine. it is due to you had given PBC. thats why. You can reset your trejectory using trjconv. regards Ravi Datta Sharma Lecturer, Bioinforma

[gmx-users] how to identify the hydrophobic core residue to calcuate gyration

Hello guys, neone have idea how to mark which are the hydrophobic residue to supply with make index command and have to calculate the gyration curve. regards, Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/___

[gmx-users] rmsd calculation of helix only

Hello everyone is there any idea how can i calculate rmsd for a given helix or all helix in a protein from a trejectory??? -Ravi Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut   Send fr

Re: [gmx-users] Re: Protein coming out of the box

water box.So thats why I have suggested, If I say wrong answer regret for that > Hi, > Ravi > Use comm_grps = protein in your .mdp file. > > > 3. protein coming out of the box (ravi sharma) > No! You will ruin energy conservation... > > Hello everyon

[gmx-users] protein coming out of the box

Hello everyone my protein coming out of the box in final md how can i fix my protein in the middle of the box. can you help me out?? Thanks Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut

[gmx-users] Fatel error in simulated annealing

Hello guys, i am doing a simulation with simulated annealing of a protein which contains heme inside, the normal without simulated annealing its running fine but while m writing simulated annealing in my md.mdp its showing error Fatal error: Not enough annealing values: 1 (for 4 groups) I am at

Re: [gmx-users] g_energy

Hi, RMSD is your just deviation of backbone from native stare while RMS fluctuation shows the per atom deviation throughout simulation. regards, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut

[gmx-users] regarding changing tempreature

Hello guys can anyone have how to do a unfolding simulation if with gradually changing the temperature 300K to 500K. Thanks, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut   Did

[gmx-users] about connections

hello guys,   is there any idea how to extract no. of connections from trejectory? Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut   Check out the all-new face of

[gmx-users] how to extend 1ns Unfolding simulation to 6ns

Hello guys, i have a problem that on unfolding simulation my protein unfolds quickly within 500ps 70% and rest stable in entire simulation as this is the state of equilibrium in which gromacs equilibrate the system ,so we wann'a do an equilibrium MD for 1ns than have to extend to 6ns, it looks