[gmx-users] simulation crashed because of LINCS error
Justin A. Lemkul
jalemkul at vt.edu
Mon May 24 12:58:09 CEST 2010
sonali dhindwal wrote:
> Thanks Mark for the reply,
> I think I have mistakenly written 30 instead of 300 for ref_t in temp
> coupling,
> So if that could be the problem ?
>
> because I have equilbrated the protein before simulation but time is
> for 20 ps. Is that very short time period?
>
> Acually I want to stress here that i have energy minimized the protein
> by restraining the positions as i mentioned before to not to have large
> changes in the protein structure, and then again equilibration and
> simulation was carried our by constraining all the bonds. So if that is
> ok to do ?
>
I remember your rationale for restraints during EM was to avoid distortions in
the structure, and the consensus that you got was that there was nothing wrong
with your results. Restraints actually serve to prevent atoms from moving, thus
defeating the purpose of EM. Repeat the EM without restraints. Your structure
is likely not sufficiently energy-minimized to continue.
-Justin
> Regards
>
> --
> Sonali Dhindwal
>
>
> --- On *Mon, 24/5/10, Mark Abraham /<mark.abraham at anu.edu.au>/* wrote:
>
>
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] simulation crashed because of LINCS error
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Monday, 24 May, 2010, 1:00 PM
>
> ----- Original Message -----
> From: sonali dhindwal <sonali11dhindwal at yahoo.co.in
> </mc/compose?to=sonali11dhindwal at yahoo.co.in>>
> Date: Monday, May 24, 2010 14:32
> Subject: [gmx-users] simulation crashed because of LINCS error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>>
>
> -----------------------------------------------------------
> | > Hello All,
> >
> > With regard to my previous post
> > http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html
> > I have done postion restrained energy minimisation using
> POSRES.itp file obtained from pdb2gmx. so that there should not be
> any large change in the strucutre of the protein.
>
> Note that there are further general recommendations about system
> preparation here
> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation,
> i.e. consider not going immediately to your target ensemble.
>
> Also, your temperature-coupling is broken in your second .mdp file.
>
> Mark
>
> > And after that I did equilbration using following mdp file
> >
> > title = protein
> > cpp = /usr/bin/cpp
> > define = -DPOSRES
> > constraints = all-bonds
> > integrator =
> md
> > dt = 0.002 ; ps !
> > nsteps = 10000 ; total 20.0 ps.
> > nstcomm = 1
> > nstxout = 250 ; collect data every 0.5 ps
> > nstvout = 1000
> > nstfout = 0
> > nstlog = 10
> > nstenergy = 10
> > nstlist =
> 5
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw = 1.4
> > 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 in two groups
> > Tcoupl = V-rescale
> > tc-grps = Protein Non-Protein
> > tau_t = 0.1 0.1
> > ref_t = 300 300
> > ; Pressure coupling is on
> > Pcoupl = berendsen
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocites is on at 300
> K.
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> >
> > After this, I put the molecule for simulation using the following
> .mdp file
> >
> > title = protein
> > cpp = /usr/bin/cpp
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 500000 ; total 1000 ps, 1
> ns.
> > nstcomm = 1
> > nstxout = 500 ; collect data every 1 ps
> > nstvout = 0
> > nstfout = 0
> > nstlist = 5
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw =
> 1.4
> > 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 in two groups
> > Tcoupl = V-rescale
> > tc-grps = Protein Non-Protein
> > tau_t = 0.1 0.1
>
> > ref_t = 300 30
> > ; Pressure coupling is on
> > Pcoupl = berendsen
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocites is on at 300 K.
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> >
> > but simulation has crashed showing the error too many Too many
> LINCS warnings (1000)
> > I checked previous
> posts, it is given that it may be due to incomplete equilibration or
> putting so many constraints.
> > So can you please help me in correcting it.
> > Thanks and regards.
> >
> > --
> > Sonali Dhindwal |
> -----------------------------------------------------------
> >
> > --
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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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