[gmx-users] Membrane simulation npt problem

[Marco Franzoi]

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.

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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