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.abra...@gmail.com>
To: gmx-us...@gromacs.org; mohammad.r0...@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.henriq...@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.henriq...@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.r0...@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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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.
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