On 2/20/15 1:01 PM, HANNIBAL LECTER wrote:
Just out of curiosity what does -0.1 actually mean?
It means someone made a mistake :) It's not physically sensible. tau-t should
be a positive decimal or -1 to turn off coupling for that group. Using -0.1
doesn't make any sense. It's probably the primary reason for failure here.
-Justin
On Fri, Feb 20, 2015 at 8:48 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/20/15 6:51 AM, Kalyanashis Jana wrote:
Dear all,
I am doing an MD simulation of a protein system. Energy minimization step
has been completed smoothly but the position restraint MD run is not
running properly(after 500-900 steps have been stopped automatically).
Even
it has not shown any error or anything. I have used a drug molecule in the
cavity of the active site.
When the box size was 10 X 12 X 25, it was run only 100 steps and with 15
X
15 X 28 box size it was run 500-900 steps. I could not understand what is
the problem. Can anyone please help me?
The pr.mdp file is
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 1000000 ; total 1000.0 ps.
nstcomm = 100
nstxout = 250 ; ouput coordinates every 0.5 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 100
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; V-rescale temparature coupling is on
Tcoupl = V-rescale
tau_t = 1.0 1.0 -0.1 1.0 1.0
tc_grps = SOL NA protein DRG CL
ref_t = 300 300 300 300 300
This thermostat setup is nonsensical.
http://www.gromacs.org/Documentation/Terminology/
Thermostats#What_Not_To_Do
-Justin
; Pressure coupling is on
pcoupl = berendsen ; Use Parrinello-Rahman for research work
pcoupltype = isotropic ; Use semiisotropic when working with
membranes
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord-scaling = all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Thanks in advance,
Kalyanashis Jana.
--
==================================================
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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==================================================
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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