[gmx-users] Membrane simulation npt problem

[Justin Lemkul]

On 1/18/16 8:13 AM, Marco Franzoi wrote:
> Thanks Justin, I've checked again all the steps. At the end the problem is
> in the nvt step. It looks like the two membrane leaflet tends to separate
> during the simulation. From here the problem with the npt.
>

Leaflet separation during NVT is pretty common and should be resolved by 
sufficient NPT equilibration.  If it is a rather large perturbation that does 
not resolve, apply restraints to the P atoms in the z-dimension to inhibit 
separation.

-Justin

> I'm still working on the problem, this is the nvt.mdp file:
>
> title = NVT equilibration
>
> define = -DPOSRES ; position restrain the protein
>
> ; Run parameters
>
> integrator = md ; leap-frog integrator
>
> nsteps = 50000  ;
>
> dt = 0.002 ; 2 fs
>
> ; Output control
>
> nstxout = 1000 ;
>
> nstvout = 1000 ;
>
> nstenergy = 1000 ;
>
> nstlog = 1000 ;
>
> ; Bond parameters
>
> continuation = no ; first dynamics run
>
> constraint_algorithm = lincs ; holonomic 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 cels
>
> nstlist = 5 ; 10 fs
>
> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
>
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
>
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
>
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>
> pme_order = 4 ; cubic interpolation
>
> fourierspacing = 0.16 ; grid spacing for FFT
>
> ; Temperature coupling is on
>
> tcoupl = V-rescale ; modified Berendsen thermostat
>
> tc-grps = Protein_PCA POPG_POPE Water_and_ions; three coupling groups -
> more accurate
>
> tau_t = 0.1 0.1 0.1 ; time constant, in ps
>
> ref_t = 315 315 315 ; reference temperature, one for each group, in K
>
> ; Pressure coupling is off
>
> pcoupl = no ; no pressure coupling in NVT
>
> ; Periodic boundary conditions
>
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
>
> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> ; Velocity generation
>
> gen_vel = yes ; assign velocities from Maxwell distribution
>
> gen_temp = 315 ; temperature for Maxwell distribution
>
> gen_seed = -1 ; generate a random seed
>
> ; COM motion removal
>
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
>
> nstcomm = 1
>
> comm-mode = Linear
>
> comm-grps = Protein_PCA_POPG_POPE Water_and_ions
>
> Marco FRANZOI
> PhD Student
> University of Padua
> Department of biology, V floor South
> Tel: 3405086908
> Mail: marco.franzoi89 at gmail.com
>
> On Sat, Jan 16, 2016 at 1:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/15/16 12:56 PM, Marco Franzoi wrote:
>>
>>> Good evening to everyone.
>>>
>>> I've an issue regarding a membrane simulation.
>>> I've downloaded an already equilibrated POPE/POPG membrane and, to test
>>> the
>>> system, I run an em, a 0.1 ns nvt and 1 ns npt simulation and everything
>>> was fine.
>>>
>>> Then, I've raised the cell lenght in the z direction and added a peptide,
>>> solvate, ionized and minimized. The next ntv step was also fine but, when
>>> I
>>> run the npt simulation, suddenly the cell broadens in xy directions and
>>> shrinks in z direction.
>>>
>>> What can be wrong with it?
>>>
>>>
>> How much do the box vectors change?  Some change is, of course, expected.
>>
>> My npt.mpd file is attached.
>>>
>>>
>> Please provide the text of the .mdp file; the mailing list does not accept
>> attachments.
>>
>> -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
>>
>> ==================================================
>>
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-- 
==================================================

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

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