[gmx-users] Need some help with membrane simulation

Ali Khan akk5r at virginia.edu
Thu Jun 5 20:47:09 CEST 2014 

I am using the charmm36 force field.

*My energy minimization .mdp file:*
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps = 50000000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
vdw-type        = cutoff
vdw-modifier = Potential-shift-Verlet
cutoff-scheme = Verlet





*Temperature equilibration .mdp file:*
title = NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 0
nstvout = 0
nstenergy = 500
nstlog = 0
; 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 cells
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)
rcoulomb-switch          = 0
rvdw-switch              = 0.8
; long-range cut-off for switched potentials
rlistlong                = 1.4
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = POPC Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; 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 = No ; account for cut-off vdW scheme
; Method for doing Van der Waals
vdw-type                 = cutoff
vdw-modifier = Potential-shift-Verlet
cutoff-scheme = Verlet
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed



On Thu, Jun 5, 2014 at 2:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/5/14, 2:11 PM, Ali Khan wrote:
>
>> Hi all,
>>
>> I don't know if anyone has experienced this problem before, but I figure I
>> ask. I have several times run a simulation on a 135A x 135A POPC membrane
>> acquired fro the charmm-gui website. I wanted now to simulate one that was
>> slightly larger (150A x 150A). I made the larger membrane on charmm-gui,
>> and I did everything the same way as I did before (even used the same .mdp
>> files). After energy minimization, I get an error during my temperature
>> equilibration as follows:
>>
>> *Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.4#*
>> *Wrote pdb files with previous and current coordinates*
>>
>> *WARNING: Listed nonbonded interaction between particles 31617 and 31619*
>> *at distance 3f which is larger than the table limit 3f nm.*
>>
>> *This is likely either a 1,4 interaction, or a listed interaction inside*
>> *a smaller molecule you are decoupling during a free energy calculation.*
>> *Since interactions at distances beyond the table cannot be computed,*
>> *they are skipped until they are inside the table limit again. You will*
>> *only see this message once, even if it occurs for several interactions.*
>>
>> *IMPORTANT: This should not happen in a stable simulation, so there is*
>> *probably something wrong with your system. Only change the
>> table-extension*
>>
>> *distance in the mdp file if you are really sure that is the reason.*
>>
>>
>>
>> *-------------------------------------------------------*
>> *Program mdrun, VERSION 4.6.5*
>> *Source code file: /home/ali/Downloads/gromacs-4.6.5/src/mdlib/pme.c,
>> line:
>> 851*
>>
>> *Fatal error:*
>> *5 particles communicated to PME node 1 are more than 2/3 times the
>> cut-off
>> out of the domain decomposition cell of their charge group in dimension
>> x.*
>>
>> *This usually means that your system is not well equilibrated.*
>> *For more information and tips for troubleshooting, please check the
>> GROMACS*
>> *website at http://www.gromacs.org/Documentation/Errors
>> <http://www.gromacs.org/Documentation/Errors>*
>> *-------------------------------------------------------*
>>
>>
>> I referred to the gromacs website, and it stated that this error means
>> that
>> my system is blowing up. I have tried several things to fix it (including:
>> remaking the system on charmm-gui, running energy minimization with small
>> energy steps [emstep = 0.01, 0.001, 0.0001], energy minimizing to Fmax of
>> 100 kJ kJ/mol/nm instead of 1000, and I have done all these combinations
>> in
>> both single and double precision) and none of these methods worked. I also
>> should add that sometimes I am able to perform the temperature
>> equilibration, but then I would get the same error during the pressure
>> equilibration. I doubt it is charmm-gui, because they are usually very
>> reliable in generating membranes.
>>
>>
> On the contrary, we've had numerous reports of crashing membranes, due to
> some clashes in the starting structures.  Manual modifications to the
> coordinates of the offending atoms (fractions of an Angstrom, really)
> usually solves it.  The output of EM tells you where the maximum force is.
>  How big is this force?  What atom is it acting upon?  That's where you
> start your investigation.
>
>
>  Does anyone have any suggestions? I can post any of my input files if
>> requested.
>>
>>
> Always post an .mdp file when a run is crashing.  Membranes can be
> particularly challenging to get right; small errors in settings can have
> catastrophic consequences.
>
> -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
>
> ==================================================
>
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