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

[Mark Abraham]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>