[gmx-users] LINCS warnings at high temperature md run

Sidong Tu sidongt at g.clemson.edu
Fri Aug 12 23:20:18 CEST 2016


Hi Christopher & Mark,

My simulation worked well with the parameters given by Christopher.  The sd
integrator & lincs-order was fit in this situation while md integrator
still had lincs warnings. I'll continue my runs with sd.
Thank you very much for your help!


Best wishes,
Sidong

Message: 4
> Date: Thu, 11 Aug 2016 15:51:55 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] LINCS warnings at high temperature md run
> Message-ID:
>         <CAMNuMARr49_nYc9XTmdcL-bkAfopZrs0rFiJPJEeejwKT5f9cA@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Fundamentally, at higher temperature you have higher atomic velocities, so
> atoms move further in a step. Your simulation is only stable if you apply
> constraints, but the default settings are chosen for normal temperatures
> and thus displacements. So try the kinds of things Chris suggests.
>
> Mark
>
> On Tue, 9 Aug 2016 20:35 Christopher Neale <chris.neale at alum.utoronto.ca>
> wrote:
>
> > Try adding "lincs-order =  6" to your mdp file.
> >
> > The following settings don't give me lincs warnings at 500 K, though I
> > presume that the lincs-order is the essential part.
> >
> > constraints = all-bonds
> > lincs-iter =  1
> > lincs-order =  6
> > constraint_algorithm =  lincs
> > dt = 0.002
> > integrator = sd
> > tc_grps             =  System
> > tau_t               =  1.0
> > ld_seed             =  -1
> >
> > failing that, post your full .mdp file.
> >
> >
> >
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sidong
> Tu
> > <sidongt at g.clemson.edu>
> > Sent: 09 August 2016 14:49:03
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Cc: Chandan K Choudhury
> > Subject: [gmx-users] LINCS warnings at high temperature md run
> >
> > Dear all,
> >
> > I was trying to simulate lysozyme and polymer in water model tip3p using
> > charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU
> and
> > the system size was about 60,000 atoms. I have done equilibrium with
> > Berendsen(B) and Parrinello-Rahman(PR), and then md. The thermal
> coupling I
> > used was v-rescale.
> > I always got a LINCS warning and my job stopped during the md. Here's the
> > parameter I have used:
> > Stage  Position_Constraint  Pcoupl  gen_vel  LINCS       dt
> > nsteps
> > 1         Protein & polymer    B           yes     all bonds    0.002
> > 200,000
> > 2         Protein                    B           yes     all bonds
> > 0.002    200,000
> > 3         None                       B           yes     all bonds
> > 0.002    200,000
> > 4         None                       PR         no       all bonds
> > 0.002    50,000
> > 5         None                       PR         no       h bonds
> > 0.002    1.25e+8
> >
> > At stage 5, the md run stopped at 149 steps and showed relative
> constraint
> > deviation after LINCS.
> >
> > I have searched for this warning and there is an explanation that it
> might
> > be introduced by the bad equilibrium. Then I added a equilibrium stage
> with
> > Berendsen pressure coupling after stage 3 with LINCS constraints of h
> bonds
> > for 50,000 steps without position constraints.
> >
> > This time there was still warings with LINCS and it stopped at step 79026
> > in md:
> >
> > Step 79026, time 158.052 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 15.598468, max 1553.834961 (between atoms 15966 and 15968)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >   15941  15943   40.7    0.2082   0.1109      0.1111
> >   15945  15946   75.6    0.2551   7.7014      0.1111
> >   15945  15947   90.0    0.2299   4.2042      0.1111
> >   15949  15950   67.8    0.1543   0.1150      0.1111
> >   15949  15951   86.2    0.1658   8.9758      0.1111
> >   15966  15967   90.0    0.1111   0.2587      0.1111
> >   15966  15968  143.1    0.1111 172.7422      0.1111
> >   15970  15971   90.0    0.1111   0.1405      0.1111
> > Wrote pdb files with previous and current coordinates
> >
> > The simulation worked well with dt=0.001 without LINCS. But I still want
> to
> > find if there is a way to simulate at high temperature(500K) with
> dt=0.002
> > so that I can use less steps?
> >
> >
> > --
> > Sidong Tu
> > Department of Materials Science and Engineering
> > Clemson University
> > Phone: (213)265-6768
> > --
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