[gmx-users] DPPC/DPPE minim.mdp
jalemkul at vt.edu
Fri Aug 28 19:25:03 CEST 2015
On 8/28/15 1:23 PM, Poncho Arvayo Zatarain wrote:
> Hello, i want to simulate a 128 DPPC molecule, 3655 water molecules but with
> 25% of DPPE. I replace de 25% of 128 DPPC molecules with DPPE and i'ḿ using
> the same forcefield and topology reported by Lemkul in his KALP15 in DPPC
> tutorial. When i want to minimize the energy i use the command line: gmx
> grompp -f minim.mdp -c dppc-dppe128.pdb -p topol_dppc.top -o em.tp but the
> following error appears: Input/output error: minim.mdp. How can i solve it?
That means the file doesn't exist in the working directory.
> Is correct to use the same forcefield and topology? I'm using Gromacs 5.0.4.
> This in my minim.mdp file ; minim.mdp - used as input into grompp to generate
> em.tpr integrator = steep ; Algorithm (steep = steepest descent
> minimization) emtol = 1000.0 ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000
> ; Maximum number of (minimization) steps to perform
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions nstlist = 1 ; Frequency to update the
> neighbor list and long range forces cutoff-scheme = Verlet ns_type =
> grid ; Method to determine neighbor list (simple, grid) coulombtype =
> PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0
> ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der
> Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no)
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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