Re: [gmx-users] more than one peptide in one simulation box

shahid nayeem wrote: Hi Justin Should I try to do position restraint at 500k and then full MD simulation. Always equilibrate under the conditions you wish to use prior to collecting data under those conditions. As for whether or not your force field is even valid at such high temperature i

Re: [gmx-users] more than one peptide in one simulation box

On 28/04/10 15:13, shahid nayeem wrote: Hi Mark How one should be certain that this much trajectory is long enough to get coverged ensemble. When the observables of interest aren't changing... This is a "how long is a piece of string?"-type question. Read some literature about simulations of

Re: [gmx-users] more than one peptide in one simulation box

Hi Mark How one should be certain that this much trajectory is long enough to get coverged ensemble. Shahid On 4/27/10, Mark Abraham wrote: > > On 27/04/2010 8:58 PM, Justin A. Lemkul wrote: > >> >> >> shahid nayeem wrote: >> >>> Dear Mark >>> Following your advice I started using three peptid

Re: [gmx-users] more than one peptide in one simulation box

Hi Justin Should I try to do position restraint at 500k and then full MD simulation. shahid On 4/27/10, Justin A. Lemkul wrote: > > > > shahid nayeem wrote: > >> My peptide is 26 residue alpha helix obtained from crystal structure .pdb >> file. I am posting energy minimization, position restari

Re: [gmx-users] more than one peptide in one simulation box

On 27/04/2010 8:58 PM, Justin A. Lemkul wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I

Re: [gmx-users] more than one peptide in one simulation box

shahid nayeem wrote: My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file ref_t = 300 300 Here, you're equilibrating at 300 K... ref_t = 500 500 and here, you're ru

Re: [gmx-users] more than one peptide in one simulation box

My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file Energy minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ; Energy mi

Re: [gmx-users] more than one peptide in one simulation box

shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In

Re: [gmx-users] more than one peptide in one simulation box

Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the traj

Re: [gmx-users] more than one peptide in one simulation box

On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insert

[gmx-users] more than one peptide in one simulation box

Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf , I tried to