[gmx-users] Need some help with membrane simulation

Thu Jun 5 22:57:36 CEST 2014

Justin,

4.6.5 does not have Potential-switch-Verlet. When I added the other
changes, I still had the same error.

Are these recommendations ones that I should generally use when
implementing charmm in gromacs?

On Thu, Jun 5, 2014 at 4:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/5/14, 2:47 PM, Ali Khan wrote:
>
>> 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
>>
>
> Use rvdw-switch = 1.0.
>
>
>  ; long-range cut-off for switched potentials
>> rlistlong                = 1.4
>>
>
> Probably never had the desired effect in terms of using CHARMM force
> fields and isn't necessary.  The Verlet scheme with rlist = 1.2 should
> provide adequate buffer space.
>
>
>  ; 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
>>
>
> Use Potential-switch-Verlet.  I don't remember if this was added to the
> code in time for 4.6.5, but it works well in any of the 5.0 releases.
>
> -Justin
>
>
>  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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>>>
> --
> ==================================================
>
> 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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