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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
