[gmx-users] Re.Importance of -rcon and -dd options when

PAVAN PAYGHAN pavanapex at gmail.com
Thu Mar 15 07:36:59 CET 2012


On Wed, Mar 14, 2012 at 7:40 PM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
>
>   1. Re: Importance of -rcon and -dd options when using mdrun  with
>      mpi. (Mark Abraham)
>   2. clashes (Dariush Mohammadyani)
>   3. Re: clashes (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Mar 2012 23:21:34 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Importance of -rcon and -dd options when
>        using mdrun     with mpi.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F608D4E.10905 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote:
> >
> > Dear Gromacs Users,
> >
> > I am running mdrun on single node with 8 CPU and getting following error
> >
> > Fatal error:-
> >
> > D D cell  1 0 0 could only obtain 1520 of the 1521 atoms that are
> > connected via constraints from the neighbouring cells.
> >
> > This probably means your constraint length are too long compared to
> > the domain decomposition cell size.
> >
> > Decrease the number of domain decomposition grid cells or lincs order.
> >
>
> The .log file has a detailed analysis of how DD is setting things up.
> You need to make sure that this output is sensible for your system.
>
> You should also desist from using P-R pressure coupling during
> equilibration (i.e. with velocity generation), as warned in the manual
> section on pressure coupling. Perhaps your system is blowing up.
>
> Mark
>
>     Dear Mark,

Thanks for the reply.
 I have successfully done the equilibration run ,while doing production run
I am gettiing above error (almost after 10 ns run).
 Also It would be worth working if you explain the importance -rcon value
and other things that I have asked .

Regards,

Pavan



> > For solving this problem following are the attempts by me.
> >
> > *1] Decreasing grid cell size:-*
> >
> >  As per the suggestion in error, I tried to decrease the grid cells by
> > option -dd from 8 1 1 to 6 1 1 , it has thrown following error..
> >
> >  Fatal error:-The size of the DD grid (6) does not match the number of
> > nodes(8).
> >
> > Can you please suggest any better way to overcome this for decreasing
> > grid cell size.
> >
> > *2] -rcon option:*
> >
> > What is the correlation between the -rcon value with DD cell
> > size(Directly or inversely proportional ) , for the problem entitled
> > above what should be the strategy (to decrease or to increase rcon
> value).
> >
> > If one changes the -rcon value will it affect the lincs accuracy, or
> > in other words the run will hold the same continuation or any change
> > in it.
> >
> > For changing the -rcon value the reference of previous log file i.e.
> > Estimated maximum distance required for p-lincs say 0.877, so one can
> > increase than what has been estimated.
> >
> > *3] lincs_order and lincs_iter :*
> >
> > **
> >
> > If we don't want to deteriorate the lincs accuracy (1+
> > lincs_iter)*lincs_order has to remain constant , In my case
> >
> > With lincs_order = 4 and lincs_iter =1 I got above error. So I
> > decreased lincs _order (2) and increased lincs_iter(3) proportionally.
> > What I am following is right or I have misunderstood it. If so please
> > correct it. Can this value be fraction?
> >
> > Values which I have tried are relevant or very bad?**
> >
> > Please explain it.
> >
> > If the same problem can be solved by any other methodology please
> > explain it.
> >
> > *Please see the mdp file  details.*
> >
> >
> > integrator        = md
> >
> > nsteps             = 10000000
> >
> > dt                         = 0.002                   ; 2 fs
> >
> > ; Output control
> >
> > nstxout                        = 1000                        ; save
> > coordinates every 2 ps
> >
> > nstvout                        = 1000                        ; save
> > velocities every 2 ps
> >
> > nstxtcout         = 1000                        ; xtc compressed
> > trajectory output every 2 ps
> >
> > nstenergy       = 1000                        ; save energies every 2 ps
> >
> > nstlog              = 1000                        ; update log file
> > every 2 ps
> >
> > ; Bond parameters
> >
> > continuation   = yes                   ; Restarting after NPT
> >
> > constraint_algorithm = lincs ; holonomic constraints
> >
> > constraints     = all-bonds             ; all bonds (even heavy atom-H
> > bonds)
> >
> > lincs_iter         = 1                               ; accuracy of LINCS
> >
> > lincs_order     = 4
> >
> > ; Neighborsearching
> >
> > ns_type                       = grid
> >
> > nstlist              = 5
> >
> > rlist                  = 1.2
> >
> > rcoulomb        = 1.2
> >
> > rvdw                = 1.2
> >
> > ; Electrostatics
> >
> > coulombtype  = PME
> >
> > pme_order     = 4
> >
> > fourierspacing           = 0.16
> >
> > ; Temperature coupling is on
> >
> > tcoupl              = Nose-Hoover
> >
> > tc-grps                        = Protein  P    SOL_NA_CL ; three
> > coupling groups - more accurate
> >
> > tau_t                = 0.5   0.5       0.5
> >
> > ref_t                = 323 323     323
> >
> > group, in K
> >
> > ; Pressure coupling is on
> >
> > pcoupl             = Parrinello-Rahman     ; Pressure coupling on in NPT
> >
> > pcoupltype     = semiisotropic                         ; uniform
> > scaling of x-y box vectors, independent z
> >
> > tau_p              = 2.0                                   ; time
> > constant, in ps
> >
> > ref_p               = 1.0   1.0                           ; reference
> > pressure, x-y, z (in bar)
> >
> > compressibility = 4.5e-5       4.5e-5 ; isothermal compressibility,
> bar^-1
> >
> > ; Periodic boundary conditions
> >
> > pbc                      = xyz                        ; 3-D PBC
> >
> > ; Dispersion correction
> >
> > DispCorr        = EnerPres    ; account for cut-off vdW scheme
> >
> > ; Velocity generation
> >
> > gen_vel                       = yes
> >
> > **
> >
> > Pavan
> >
> >
>
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> ------------------------------
>
> Message: 2
> Date: Wed, 14 Mar 2012 10:03:31 -0400
> From: Dariush Mohammadyani <d.mohammadyani at gmail.com>
> Subject: [gmx-users] clashes
> To: gmx-users at gromacs.org
> Message-ID:
>        <CAAk3nxd6rq2Y2QD5be9sK+b=ay9Nb6Z+1Nc-UfSHPiMLMv7uRw at mail.gmail.com
> >
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>
> Dear user,
>
> When I am using:
> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro
>
> to add water in a coarse grained system, after running mdrun I am getting
> "Syntax error" and it shows maybe the distances are so close or there are
> some clashes.
>
> Do you know how can I figure it out?
> Or actually if we have some clashes in system how we can correct them?
>
> Thanks,
> Dariush Mohammadyani
> Department of Structural Biology
> University of Pittsburgh School of Medicine
> Biomedical Science Tower 3
> 3501 Fifth Avenue
> Pittsburgh, PA 15261
> USA
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> ------------------------------
>
> Message: 3
> Date: Wed, 14 Mar 2012 10:08:49 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] clashes
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F60A671.4030105 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Dariush Mohammadyani wrote:
> > Dear user,
> >
> > When I am using:
> > genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro
> >
> > to add water in a coarse grained system, after running mdrun I am
> > getting "Syntax error" and it shows maybe the distances are so close or
> > there are some clashes.
> >
>
> I've never heard of mdrun throwing a syntax error.  Can you please copy and
> paste the complete error message from your terminal?
>
> > Do you know how can I figure it out?
> > Or actually if we have some clashes in system how we can correct them?
> >
>
> Better energy minimization typically solves bad atomic clashes.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
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