Re: [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.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  = 5 ; 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.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [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.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          = 5         ; 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
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Re: [gmx-users] mdp options in GROMACS 4.5.5

[Mark Abraham]

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 
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,  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  = 5 ; 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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> >
> --
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> posting!
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Re: [gmx-users] mdp options in GROMACS 4.5.5

[João Henriques]

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  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,  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  = 5 ; 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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
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Re: [gmx-users] mdp options in GROMACS 4.5.5

[João Henriques]

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,  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  = 5 ; 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] mdp options in GROMACS 4.5.5

[‪Mohammad Roostaie‬ ‪]

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  = 5 ; 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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