[gmx-users] LINCS warning in md run

Wed Sep 12 21:39:53 CEST 2012

Hi Justin,
my mdp file for the md run looks like this:

define          = -DPOSRES
integrator              = md
dt                      = 0.001
nsteps          = 5000
nstxout         = 100
nstvout         = 0
nstfout         = 0
nstlog          = 1000
nstxtcout               = 500
nstenergy               = 5
energygrps              = Protein Non-Protein
nstcalcenergy   = 5
nstlist         = 10
ns-type         = Grid
pbc                     = xyz
rlist           = 0.9
coulombtype             = PME
rcoulomb                = 0.9
rvdw            = 0.9
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
gen_vel         = yes
gen_temp                = 200.0
gen_seed                = 9999
constraints             = all-bonds
tcoupl          = V-rescale
tc-grps         = Protein  System_&_!Protein
tau_t           = 0.1     0.1
ref_t           = 298     298
pcoupl          = no
freezegrps = Protein_&_!TYP
freezedim = Y Y Y

I added a phosphate (TYP) to my protein and now want to do first a
minimization (which I already did), then a short md run (for the case that
I am in a local minima) and after that again a minimization.
Since I only want to minimize the energy of the phosphate I freezed the
rest of the protein (Protein_&_!TYP).

Since on my cluster I am not allowed to run long jobs I had to divide the
minimization run in several runs. The output of the last run was:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -7.7264606e+05
Maximum force     =  1.6227990e+04 on atom 961
Norm of force     =  1.2328220e+02

gcq#192: "It's So Fast It's Slow" (F. Black)

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -7.7264606e+05
Maximum force     =  1.6227990e+04 on atom 961
Norm of force     =  1.2328220e+02

After this minimization run I wanted to do the md run.

My protein is a membrane protein with its surrounding membrane. I already
did a minimization and md run with this protein but without the phosphate.
The only difference to the time when everything worked fine is the
phosphate.

Does this help you somehow to see the failure?

Thank you!!

>
>
> On 9/12/12 6:57 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> during the mdrun_mpi I get many LINCS warnings like for example:
>>
>> Step 1143, time 1.143 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.265373, max 1.416702 (between atoms 976 and 979)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>      976    979   90.0    0.1072   0.2320      0.0960
>>
>>
>> But I don't know why. I already minimized my protein. And also in the
>> grompp run there were no error messages. This was the end of my grompp
>> output:
>>
>>
>> processing index file...
>> Making dummy/rest group for Acceleration containing 80212 elements
>> Making dummy/rest group for Freeze containing 51274 elements
>> Making dummy/rest group for VCM containing 80212 elements
>> Number of degrees of freedom in T-Coupling group System is 102623.00
>> Making dummy/rest group for User1 containing 80212 elements
>> Making dummy/rest group for User2 containing 80212 elements
>> Making dummy/rest group for XTC containing 80212 elements
>> Making dummy/rest group for Or. Res. Fit containing 80212 elements
>> Making dummy/rest group for QMMM containing 80212 elements
>> T-Coupling       has 1 element(s): System
>> Energy Mon.      has 2 element(s): Protein non-Protein
>> Acceleration     has 1 element(s): rest
>> Freeze           has 2 element(s): Protein_&_!TYP rest
>> User1            has 1 element(s): rest
>> User2            has 1 element(s): rest
>> VCM              has 1 element(s): rest
>> XTC              has 1 element(s): rest
>> Or. Res. Fit     has 1 element(s): rest
>> QMMM             has 1 element(s): rest
>> Checking consistency between energy and charge groups...
>> Estimate for the relative computational load of the PME mesh part: 0.32
>> writing run input file...
>>
>>
>> Can you please help me?
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Without a complete description of your system (its contents, previous
> minimization and equilibration and their success/failure) and any relevant
> .mdp
> file(s), there's little else that anyone can say.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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