[gmx-users] free energy caculation error

[Justin Lemkul]

On 4/9/14, 6:41 AM, jane wrote:
> Hi all,
> I want to caculate the free energy of a molecule, but when I run the MD, it
> appears the error: "There is no domain decomposition for 8 nodes that is
> compatible with the given box and a minimum cell size of 4.44444 nm. Change
> the number of nodes or mdrun option -rdd or -dds".However, even though i
> added the -rdd and -dds, the error is same as the previous. my mdp file as
> follows.
>

Use fewer processors.  Not all systems can be decomposed into any arbitrary 
number of DD cells; there are limits related to cell size.  Your system is too 
small to be effectively split over 8 nodes.

-Justin

> ; we'll use the sd integrator
> ;run parameters
> integrator          =  sd
> dt                  =  0.002	                   ; ps
> nsteps              =  5000	               ; total 1ns
> nstcomm             =  100
>
> ; turn off trajectory writing
> nstxout			 = 0
> nstvout			 = 0
> ; cut-offs at 1nm
> rlist                    = 1.0
> nstlist                  = 10
> coulombtype              = pme
> vdw-type                 = cut-off
> rvdw                     = 1.0
> constraints              = all-bonds
> ; set temperature to 300K
> tcoupl                   = v-rescale
> tc-grps                  = system
> tau-t                    = 0.2
> ref-t                    = 300
> ; and pressure to 1 bar
> pcoupl			 = parrinello-rahman
> ref-p			       = 1
> compressibility		 = 4.5e-5
> tau-p			       = 5
> ; and set the free energy parameters
> free-energy              = yes
> couple-moltype           = RNA_chain_A
> init-lambda              = 0
> ; these 'soft-core' parameters make sure we never get overlapping
> ; charges as lambda goes to 0
> sc-power                 = 1
> sc-sigma                 = 0.3
> sc-alpha                 = 1.0
> ; we still want the molecule to interact with itself at lambda=0
> couple-intramol          = no
> couple-lambda1           = vdwq
> couple-lambda0           = none
> foreign-lambda           = 0 0.2 0.4 0.6 0.8 0.9 1
> nstdhdl                  = 10
> separate-dhdl-file       = yes
> dhdl-derivatives         = yes
> dh_hist_size             = 5
> dh_hist_spacing          = 50
>
> thanks for advances.
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-caculation-error-tp5015758.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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