[gmx-users] high temperature during mdrun

[Justin Lemkul]

On 5/24/17 8:52 AM, fatemeh ramezani wrote:
>
>
>
>   Hi dear gmx-usersI am simulating gold surface- protein interaction by GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun starts, temperature reaches to 5.50769e+05 and mdrun fails. md.mdp file containe:
> title            = gold
> cpp           = cpp
> include       =
>
> ; RUN CONTROL PARAMETERS
> integrator       = md
> comm_mode  = Linear
> ;nstcomm       =  1
> ;comm_grps   = Protein  Non-protein
> ;nstcalcenergy = 1
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol       = 500.0
> emstep    = 0.001
> tinit          = 0.000
> dt             = 0.0005
> nsteps      = 100000
>
> ; OUTPUT CONTROL OPTIONS
> nstxout     = 3000
> nstvout     = 3000
> nstfout      = 0
> nstlog       = 1
> nstenergy         = 3000
>
> ; Output frequency and precision for xtc file
> nstxtcout  = 3000
> xtc-precision    = 3000
>
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> pbc      = xyz
> periodic_molecules    = yes
> ; nblist cut-off
> rlist                   = 1.10
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype     = PME
> r_coulomb        = 1.1
> ;pme_order       = 6
> ;fourierspacing   = 0.10
> ewald_rtol        = 1e-06
> ewald_geometry          = 3d
>
> ; Method for doing Van der Waals
> vdw-type             = switch
> ; cut-off lengths
> rvdw-switch           = 0.90
> rvdw                     = 1.10
>
> ; OPTIONS FOR BONDS
> constraints   = none
> constraint-algorithm  =  Lincs
> lincs-order           = 8
> lincs-iter               = 12
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle     = 90
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl            = Nose-Hoover
> nhchainlength   = 1
> ; Groups to couple separately
> tc-grps                 = Protein  SOL NA CL     slab AUC

Do not do this.

http://www.gromacs.org/Documentation/Terminology/Thermostats

> ; Time constant (ps) and reference temperature (K)
> tau-t                    =  0.2 0.2 0.2 0.2 0.2  0.2
> ref-t                     =  300 300 300 300 300 300
>
> ; Non-equilibrium MD stuff
> freezegrps            = slab
> freezedim             = Y Y Y
>
> Can anyone help me to solve this problem?thank you in advance
>

Your system is blowing up.  Follow the standard advice at

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System 


as well as the cautionary notes about using freezing and required energy group 
exclusions at

http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#non-equilibrium-md

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================