[gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

[Steven Neumann]

Or just to switch to NVT? I guess it would be less realistic if one wants
to study extract the most likely conformation...


On Tue, May 13, 2014 at 3:26 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> What would you recommend then? Equilibrate with Berendsen barostat and
> v-rescale thermostat?
>
>
> On Mon, May 12, 2014 at 2:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/12/14, 3:58 AM, Steven Neumann wrote:
>>
>>> Dear Gmx Users,
>>>
>>> I am running REMD of a small protein in water. I have 36 temperatures.
>>> After minimization I equilibrate each with nvt and npt ensemble. Then I
>>> start REMD with -multidir. The mdp:
>>>
>>>
>>> ; Run parameters
>>> integrator  = md        ; leap-frog integrator
>>> nsteps      = 50000000
>>> dt          = 0.002     ; 2 fs
>>> ; Output control
>>> nstxout     = 0       ; save coordinates every 0.2 ps
>>> nstvout     = 0       ; save velocities every 0.2 ps
>>> nstenergy   = 5000       ; save energies every 0.2 ps
>>> nstxtcout   = 5000
>>> nstlog      = 5000
>>> ; Bond parameters
>>> continuation    = no           ; first dynamics run
>>> constraint_algorithm = lincs    ; holoyesmic constraints
>>> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
>>> constrained
>>> lincs_iter      = 1             ; accuracy of LINCS
>>> lincs_order     = 4             ; also related to accuracy
>>> ; Neighborsearching
>>> ns_type     = grid      ; search neighboring grid cells
>>> nstlist     = 5         ; 10 fs
>>> vdwtype     = Switch
>>> rvdw-switch = 1.0
>>> rlist       = 1.4       ; short-range neighborlist cutoff (in nm)
>>> rcoulomb    = 1.4       ; short-range electrostatic cutoff (in nm)
>>> rvdw        = 1.2       ; short-range van der Waals cutoff (in nm)
>>> ewald_rtol  = 1e-5      ; relative strenght of the Ewald-shifted
>>> potential
>>> rcoulomb
>>> ; Electrostatics
>>> coulombtype     = PME       ; Particle Mesh Ewald for long-range
>>> electrostatics
>>> pme_order       = 4         ; cubic interpolation
>>> fourierspacing  = 0.12      ; grid spacing for FFT
>>> ; Temperature coupling is on
>>> tcoupl      = V-rescale                     ; modified Berendsen
>>> thermostat
>>> tc_grps     = Protein Water_and_ions   ; two coupling groups - more
>>> accurate
>>> tau_t       = 0.1   0.1                     ; time constant, in ps
>>> ref_t       = 320.12   320.12                     ; reference
>>> temperature,
>>> one for each group, in K
>>> ; Pressure coupling is on
>>> pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
>>> NPT
>>> pcoupltype  = isotropic                     ; uniform scaling of box
>>> vectors
>>> tau_p       = 2.0                           ; time constant, in ps
>>> ref_p       = 1.0                           ; reference pressure, in bar
>>> compressibility = 4.5e-5                    ; isothermal compressibility
>>> of
>>> water, bar^-1
>>> refcoord_scaling = com
>>> ; Periodic boundary conditions
>>> pbc         = xyz       ; 3-D PBC
>>> gen_temp    = 320.12
>>> DispCorr    = EnerPres  ; account for cut-off vdW scheme
>>> gen_seed   = 173529
>>> gen_vel     = yes       ; assign velocities from Maxwell distribution
>>>
>>>
>>> I get the error: step 12005: Water molecule starting at atom 7030 can not
>>> be settled. I tried to repeat it and I get the same error with another
>>> water molecule at different step. I am using Gmx 4.5.5
>>>
>>> I tried minimization many times lowering the maximum force by steepest
>>> descent, make the time step 1fs in equilibtration but it does not help. I
>>> changed to force field as well and the same is happening. Please, advise.
>>>
>>>
>> NPT REMD is often unstable because when switching the configurations
>> between conditions, the barostats can become unstable.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> 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.
>>
>
>