[gmx-users] mdp options in GROMACS 4.5.5

[‪Mohammad Roostaie‬ ‪]

Dear Mark,
I was using version 5.1.4, but I got this error when using "gmx mdrun":
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted

I tried version 5.0.4, too, and I got the same error. Hence, I decided to use the 4.5.5 version which does not give me that error.
Mohammad

      From: Mark Abraham <mark.j.abraham at gmail.com>
 To: gmx-users at gromacs.org; mohammad.r0325 at yahoo.com 
 Sent: Wednesday, 7 June 2017, 13:02:46
 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5
   
Hi,You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-)Mark
On Tue, 6 Jun 2017 17:49 João Henriques <joao.m.a.henriques at gmail.com> wrote:

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
mean, not the integration).

/J

On Tue, Jun 6, 2017 at 5:45 PM, João Henriques <joao.m.a.henriques at gmail.com
> wrote:

> Hi!
>
> I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> manual for that version (or the closest one).
>
> Cheers,
>
> /J
>
> On Tue, Jun 6, 2017 at 3:27 PM, <mohammad.r0325 at yahoo.com> wrote:
>
>> Hi All,
>> I have used below mdp options in GROMACS version 5.0.4. ; 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)Now, I want to use it in GROMACS version 4.5.5. But I got the error
>> which said that the cutoff-scheme is not recognized. what should I write
>> instead of "cutoff-scheme" in this version?
>> Thanks,Mohammad
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