[gmx-users] mdp options in GROMACS 4.5.5

[Justin Lemkul]

On 6/7/17 10:05 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> 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.

If you're having a problem with a specific version, you should try something 
*newer* rather than significantly older.  Your posts about that issue went 
unresolved because there's not nearly enough information about what you did to 
install 5.1.4 (hardware, OS, compilers, your cmake command, etc).

Try with 2016.3 for something modern and actively being maintained.  It's a lot 
more effective for the developers to troubleshoot issues with the current 
version than one that is not even officially supported any more.

-Justin

> 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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>>
>>
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> 
>     
> 

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================