[gmx-users] Placing a peptide above aqueous phase of bilayer

Dear users, I want to place the peptide above aqueous phase of the bilayer.I have gone throught the mailing list and read the manual also, but since am a beginner to gromacs it will be very helpful if someone could mail me the commands to insert peptide above bilayer.I understood that it can be

[gmx-users] MD parameters for DPPC bilayer

dear users, Can anyone send me the Md parameters(.mdp file) for dppc molecule with 12lipids and 3655 water molecules that worked without any errors like "pressure scaling not more than 1%" and more?It will be very helpful as i will check out that with my mdp file. Thanks in advance __

[gmx-users] segmentation fault after mdrun

Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the accuracy.But then the simulation is not getting completed.Its taking hours together.Normally what's the running time for a lipid bilayer?I dint find anyt

[gmx-users] segmentation fault after mdrun

Hello sir, Thanks for your suggestion.Then as u suggested i start the work from scratch and did the equilibriation again, there is nothing wrong with the topology also because it was taken from tiemann's website.The only message that it gives after equlibriation run is "Steepest Descents converg

[gmx-users] Error after Mdrun

Dear all, I need some help in my simulation. I Put system(dppc bilayer) in a cubic box then solvated it and made a equlibriation run.There were no issues till then.But when i proceded with the production run , the simulation crashes in no more than 5 or 10 steps leaving an error message saying