[gmx-users] Need some help with membrane simulation

Justin Lemkul jalemkul at vt.edu
Thu Jun 5 22:31:44 CEST 2014 


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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