[gmx-users] EM curve question

2011-12-21 Thread parto haghighi
Dear Mark, Thanks for your answer. I have done these steps: 1. Prepare ligand topology by PRODRG server (like fifth gromacs tutorial) 2. Download lipid.itp file and make new force field for it (like second gromacs tutorial) 3. Use editconf and cat to prepare a system with 12 ligand in both sides

Re: [gmx-users] EM curve question

2011-12-21 Thread Justin A. Lemkul
parto haghighi wrote: Dear Mark, Thanks for your answer. I have done these steps: 1. Prepare ligand topology by PRODRG server (like fifth gromacs tutorial) Did you adequately correct the parameters therein? As noted in that tutorial (and elsewhere), the charges and charge groups produced

[gmx-users] EM curve question

2011-12-20 Thread parto haghighi
Dear GMX-users I am working on lipid-drug system.I have done these stages: 1.creating topology for drug and lipid 2.solvation 3.Ion addition 4.Energy minimization 5.NVT My question is,why does the energy and temperature curves converge to zero(I have used 320 K for my temperature in mdp file)?

Re: [gmx-users] EM curve question

2011-12-20 Thread Mark Abraham
On 20/12/11, parto haghighi parto.haghi...@gmail.com wrote: Dear GMX-users I am working on lipid-drug system.I have done these stages: 1.creating topology for drug and lipid 2.solvation 3.Ion addition 4.Energy minimization 5.NVT My question is,why does the energy and temperature curves