Re: [gmx-users] Re: Step 6 of lysozyme tutorial

2010-01-30 Thread Justin A. Lemkul
bharat gupta wrote: thanks for the advice sir .. Actually I have to study how the interaction between a coiled peptide and a protein takes place through simulation .. and i am new to simulation .. i know a little theory about simulation .. so can u suggest me how to start ... and will it poss

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

2010-01-30 Thread bharat gupta
thanks for the advice sir .. Actually I have to study how the interaction between a coiled peptide and a protein takes place through simulation .. and i am new to simulation .. i know a little theory about simulation .. so can u suggest me how to start ... and will it possible to complete my work

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

2010-01-30 Thread Justin A. Lemkul
bharat gupta wrote: here is the link for that tutorial ... What link? and one more thing I wanna ask that in the tutorial he has asked to download to .mdp file (like ions.mdp) . My doubt is .. I should know the theory for creating such files for the system of my study .. That's what the

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

2010-01-30 Thread bharat gupta
here is the link for that tutorial ... and one more thing I wanna ask that in the tutorial he has asked to download to .mdp file (like ions.mdp) . My doubt is .. I should know the theory for creating such files for the system of my study .. Bharat -- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

2010-01-30 Thread Tsjerk Wassenaar
Hi Bharat, Besides the notes of Justin, which lysozyme tutorial? And for which GMX version was that tutorial written? Tsjerk On Sat, Jan 30, 2010 at 12:53 PM, Justin A. Lemkul wrote: > > > bharat gupta wrote: >> >> Hi >> >> I am getting the follwing error while running the mdrun command given >

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

2010-01-30 Thread Justin A. Lemkul
bharat gupta wrote: Hi I am getting the follwing error while running the mdrun command given in the step six of the lysozyme tutorial :- Program mdrun, VERSION 4.0.7 Source code file: gmxfio.c, line: 737 Can not open file: topol.tpr --- "

[gmx-users] Re: Step 6 of lysozyme tutorial

2010-01-30 Thread bharat gupta
Hi I am getting the follwing error while running the mdrun command given in the step six of the lysozyme tutorial :- Program mdrun, VERSION 4.0.7 Source code file: gmxfio.c, line: 737 Can not open file: topol.tpr --- "This Doesn't Suck, It's