[gmx-users] Re: Temperature decreasing with NVE MARTINI lipid simulation

[Michael Lerner]

Hi,

As mentioned in the reference below, changing rlist to 1.4 (greater than the
nonbonded cutoffs) and changing nstlist to 5 appears to solve the problem.


   1. Siewert J. Marrink et al., “Comment on “On using a too large
   integration time step in molecular dynamics simulations of coarse-grained
   molecular models” by M. Winger, D. Trzesniak, R. Baron and W. F. van
   Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934,” Physical Chemistry
   Chemical Physics 12, no. 9 (2010): 2254.


On Tue, Jun 15, 2010 at 10:44 PM, Michael Lerner <mglerner at gmail.com> wrote:

> Hi,
>
> I want to run some MARTINI DPPC/water simulations using the microcanonical
> (NVE) ensemble.
>
> I ran a long NVT simulation to make sure things were fully equilibrated.
> Then I took the .gro file as input and removed the temperature/pressure
> coupling options from my .mdp file. I also removed the
> center-of-mass-removal options. Unfortunately, the temperature decreases
> rather quickly from 323K to below 200K. I've included my .mdp file below. Is
> there something obviously wrong with it? If not, are there other things I
> should try?
>
> Thanks,
>
> -Michael
>
> P.S. I recently changed the email address that I use to subscribe to
> gmx-users. My apologies if this gets sent to the list twice as part of that.
>
> Pcoupl = no
> DispCorr = No
> gen_vel = no
> integrator = md
> nstvout = 100000
> epsilon_surface = 0
> nstlog = 2500
> nstenergy = 2500
> comm_mode = None
> xtc_precision = 100
> rvdw_switch = 0.9
> epsilon_r = 15
> nstxtcout = 2500
> ewald_rtol = 1e-05
> continuation = yes
> constraints = none
> nsteps = 500000
> vdw_type = Shift
> tcoupl = no
> rlist = 1.2
> lincs_warnangle = 30
> xtc-grps = Prot
> lincs_order = 4
> dt = 0.02
> tinit = 0.0
> coulombtype = Shift
> shake_tol = 0.0001
> nstlist = 5
> rcoulomb_switch = 0.0
> morse = no
> nstxout = 100000
> annealing = no
> constraint_algorithm = Lincs
> pbc = xyz
> rcoulomb = 1.2
> compressibility = 5e-5 5e-5
> energygrps = Prot SOL
> ns_type = grid
> nstfout = 0
> rvdw = 1.2
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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