Rabab Toubar wrote:
Hi Justin,
Thanks for the reply. When I tried to gmxcheck the minimization process
I got an error:
Timesteps at t=810 don't match (2, 1)
Timesteps at t=814 don't match (1, 2)
Timesteps at t=816 don't match (2, 1)
Timesteps at t=818 don't match (1, 2)
till the end of the run, that is why I thought the system is not
properly minimized. I will look into how to check the Potential Energy.
When running EM, mdrun prints the important information out at the very end,
both to the screen and to the end of the .log file.
the em.mdp file is as follows:
cpp = /usr/bin/cpp ; the c preprocessor
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ;ps ie 2 fs!
nsteps = 1000
nstlist = 10
ns_type = grid
rlist = 1.0 ;short range
coulombtype = cut-off
rcoulomb = 1.0
rvdw = 1.0
vdwtype = cut-off
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
emtol = 10
emstep = 0.01
the md.mdp file is:
cpp = /usr/bin/cpp
constraints = none ;*
integrator = md
dt = 0.002 ; ps !
Using a 2-fs timestep without constraints may not be stable. Your original
message said you ran 2 ns of position restrained MD with LINCS, which I assumed
meant that you were constraining the bond lengths. If you actually did this,
what reason do you have for turning off the restraints after equilibrating?
nsteps = 12500000 ; total 25 ns;*
nstcomm = 1
nstxout = 500 ; collect data every 1 ps
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = cut-off
Using a plain cutoff for electrostatics can lead to a number of artefacts. I
see no reason to use this method in favor of other, more advanced and accurate
methods.
-Justin
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0 ;*
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5 ; ps
compressibility = 4.5e-5 ; bar-1
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 621432
Any suggestions are appreciated
Thanks
Rabab Toubar
--- On *Thu, 6/3/10, Justin A. Lemkul /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] 1-4 interaction not within cut-off
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Thursday, June 3, 2010, 4:37 PM
Rabab Toubar wrote:
> Hi,
>
> I set my .mdp file to minimize the system for 1000 steps, but it
stopped at ~200 saying: "Stepsize too small, or no change in energy.
> Converged to machine precision, but not to the requested
precision Fmax < 10" but the molecule is now outside the box
>
This is not really a problem, provided that both the potential
energy and Fmax that resulted are
reasonable.http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
> I did position restraint for 2ns using LINCS, and things went well
>
> running md, it ran for only 0.3 ns out of 30, and I got an error
message that 1-4 interaction between 2 atoms are at a distance >
table-size (1nm) with a suggestion to increase the table-extension
in mdp file.
> I checked
http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
suggesting reminimizing.
>
The other possibility is that your .mdp settings are inappropriate,
but you haven't provided that information.
> My question is: is it OK that the system doesn't minimize till
the end of the specified number of steps? is it OK to be outside the
box as long as you assign boundary conditions as in case of NAMD?
and what is the best option - you think - I have to solve the md problem
>
Whether or not you need to revisit the EM procedure depends on how
well it actually did (see comment above). The periodicity effect is
a non-issue, since there is no "outside" of a periodic box.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
> Any suggestions are highly apprecitaed
> Rabab
>
>
-- ========================================
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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--
========================================
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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