[gmx-users] mdp file warnings

[Eduardo Oliveira]

OK, so if i got this right all I have to do is add another line in the mdp file with refcoord_scaling = com?  I thought that i had to make a substitution in one of the existing terms.

Thanks.


________________________________
 De: Justin Lemkul <jalemkul at vt.edu>
Para: Eduardo Oliveira <eduardobio at yahoo.com.br>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Enviadas: Segunda-feira, 17 de Dezembro de 2012 11:57
Assunto: Re: [gmx-users] mdp file warnings
 


On 12/17/12 8:55 AM, Eduardo Oliveira wrote:
> Hi,
>
> I'm setting my system but when I run grompp I get a warning and the program terminates.  It says the following:
>
> You are using  pressure coupling with absolute position restraints, this will give artifacts. Use refcoord_scaling option.
>
>
> I want to try it but i don't know where to change this term in the mdp file. Any help?
>

Location within the file is irrelevant.  For most cases, you want 
"refcoord_scaling = com."  See the numerous discussions on this topic in the 
list archive.

-Justin

> title                    = 500ps_pr_fixo
> cpp                      = /lib/cpp
> define                   = -DPOSRES
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 250000 ; total 500 ps
> comm-mode                = Linear
> nstcomm                  = 1
> nstxout                  = 500
> nstvout                  = 20000
> nstfout                  = 20000
> nstlog                   = 1000
> nstenergy                = 100
> nstxtcout                = 500
> xtc-precision            = 1000
> energygrps               = Protein SOL NA
> nstlist                  = 5
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> domain-decomposition     = no
> coulombtype              = PME
> rcoulomb                 = 1.0
> epsilon-r                = 1
> vdw-type                 = Cut-off
> rvdw                     = 1.4
> DispCorr                 = EnerPres
> optimize_fft             = yes
> Tcoupl                   = V-rescale ;berendsen
> tc-grps                  = Protein Non-protein
> tau-t                    = .1 .1
> ref-t                    = 310 310
> gen_vel                  = yes
> gen_temp                 = 310
> gen_seed                 = 173529
> Pcoupl                   = berendsen
> Pcoupltype               = Isotropic
> tau-p                    = 1
> compressibility          = 4.5e-5
> ref-p                    = 1
> constraints              = all-bonds
> constraint-algorithm     = Lincs
> unconstrained-start      = no
> Shake-SOR                = no
> shake-tol                = 1e-04
> lincs-order              = 4
> lincs-warnangle          = 30
> morse                    = no
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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