[gmx-users] simulation crashed because of LINCS error

[sonali dhindwal]

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 ?

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>
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>

-----------------------------------------------------------
| > 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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