TJ Mustard wrote:
<snip>
*Positional restraint mdp file:*
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.004 ; ps
Unless you're using virtual sites (which, per your commands below, you are not)
this time step is inappropriately large and is a likely source of instability.
With plain constraints, 2 fs is more appropriate.
nsteps = 2500 ; total ps = dt*nsteps
nstcomm = 1
nstxout = 200 ; output coordinates every ps = dt*nstxout
nstvout = 1000 ; output velocities every ps = dt*nstvout
nstfout = 0
nstenergy = 10
nstlog = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
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
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1
tc_grps = protein RNA SOL NA CL
Also a major concern - never couple solvent and ions separately! See here:
http://www.gromacs.org/Documentation/Terminology/Thermostats
ref_t = 310 310 310 310 310
; Pressure coupling is on
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocities is on at 310K (core body temp)
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
*main molecular dynamics mdp file:*
<snip>
define = -DPOSRES
Restraints during data collection, or did you paste the wrong file?
<snip>
; Generate velocities is on at 310K (core body temp)
gen_vel = yes
Re-generating velocities after equilibration defeats the whole purpose of
equilibrating. Per your commands below, you are not preserving the velocities
(grompp -t with .trr or .cpt file) obtained during your PR equilibration.
gen_temp = 310.0
gen_seed = 173529
*And my script for running the whole process:*
pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top
editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5
genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top
grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b4ion.tpr
genion -s receptor_b4ion.tpr -o receptor_b4em.gro -neutral -conc 0.0001
-pname NA -nname CL -g receptor_ion.log -p receptor.top
*Here I select the SOL for ions...*
grompp -f em.mdp -c receptor_b4em.gro -p receptor.top -o receptor_em.tpr
mdrun -v -s receptor_em.tpr -c "$base"_after_em.gro -g emlog.log
grompp -f pr.mdp -c receptor_after_em.gro -p receptor.top -o receptor_pr.tpr
mdrun -v -s receptor_pr.tpr -o receptor_pr.trr -e pr.edr -c
receptor_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt
grompp -f md.mdp -c receptor_after_pr.gro -p receptor.top -o receptor_md.tpr
mdrun -s receptor_md.tpr -o receptor_md.trr -c receptor_after_pr.gro -g
md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt
*Where receptor is of course my protein/RNA pdb name*
I always make sure that the pdb doesn't give me notes or warnings or
errors of course in the pdb2gmx step. Most of the time I minimize to my
computers "machine precision."
**
*This is the return I get from the "EM" step:*
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 200
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 324 steps,
but did not reach the requested Fmax < 200.
Potential Energy = -1.9868888e+07
Maximum force = 8.7276396e+03 on atom 19080
This is a very high Fmax, indicating that you have bad clashes in your system
that, when combined with the parameters above, surely leads to an unstable
system. The fact that Gromos96 works is a bit curious, but you have too many
potential pitfalls listed here to specifically diagnose the difference based on
this information alone.
-Justin
Norm of force = 3.8592850e+01
*I will get this error sometime in the "PR" step of my script:*
step 0
Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053
0.849053
Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053
0.849053
Step 22, time 0.088 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005723, max 0.026407 (between atoms 6545 and 6542)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
I hope this is enough information. Any help would be much appreciated.
TJ Mustard
Email: musta...@onid.orst.edu
Cell: 509-879-4173
On September 9, 2010 at 9:11 PM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
>
>
> TJ Mustard wrote:
> >
> > First off I am using gromacs 4.5. I will also post all of my files and
> > errors if they help.
> >
> >
> >
> > If I run a protein in GROMOS96 all my md runs complete succesfully. But
> > if I change to any of the AMBER force fields I get LINCS errors in my
> > positional restraint md run. I have tried using shake, 1 fs step sizes,
> > -heavyh, and many more. Does anyone know what is going on here?
> >
>
> A complete (but not overly lengthy) post will save everyone a lot of
time.
> Based on the information you've provided here, I see now way to
diagnose the
> problem. The most important information to post would be your .mdp file.
> Certain settings can influence stability. A description of the hardware,
> compilers used, etc. can also be useful.
>
> -Justin
>
> >
> >
> > The reason I want to use AMBER is the fact that I want to run md on the
> > 30s rybosome and amber converts RNA much easier than GROMOS force
fields.
> >
> >
> >
> >
> >
> > Thank you in advance,
> >
> >
> >
> > TJ Mustard Email: musta...@onid.orst.edu
> > Cell: 509-879-4173
> >
> >
> >
> >
>
> --
> ========================================
>
> 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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