[gmx-users] Acetonitrile using CHARMM ff

[Justin Lemkul]

On 7/10/17 10:52 AM, Sonia Milena Aguilera Segura wrote:
> Dear Justin,
> 
> Thank you for the answer. I changed the two parameters suggested in the mdp file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for the two cases of the previous mail, and now I am getting densities around 771 g/m3 which is slightly underestimated, but close to what other authors have obtained (774 others and 777 experimental). Also, I got slightly higher values for dielectric constants and diffusivities, also closer to another simulation with CHARMM. The energies also changed, but I guess that was expected. It looks like reproducing the dielectric constant with the current parameters is not possible. Is there anything that can be changed in order to get a better description? In terms of simulation, what is the dielectric constant depending of?
> 

Structure, charge distribution, etc.  This may just be a limitation of an 
additive force field model.  We typically see neat liquid properties better 
reproduced with polarizable models.

> Moreover, I observed that this time I got lower values for P during the NPT equilibration, but still is too far from 1 bar.  I really don't understand why for the NVT simulation I get a T around 298, but as soon as I turn on the pcoupl, the T rises to 300-301 K and the P gets average values of 7 and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7 bar. Considering the parameters I am using, is there anything I can change to make the P coupling better? I am running a 3 nm box with 308 molecules. This is the full mdp file:
> 

http://www.gromacs.org/Documentation/Terminology/Pressure

Your box is very small and will be subject to large fluctuations.

-Justin

> ; Run control
> integrator               = sd       ; Langevin dynamics
> tinit                    = 0
> dt                       = 0.0005
> nsteps                   = 2000000   ; 1 ns
> nstcomm                  = 100
> ;energygrps		 = non-Water
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme            = verlet
> nstlist                  = 20
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.2
> ; Electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.2
> ; van der Waals
> vdwtype                  = cutoff
> vdw-modifier             = force-switch
> rvdw-switch              = 1.0
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = no
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 298.15
> ; Pressure coupling is on for NPT
> Pcoupl                   = Parrinello-Rahman
> tau_p                    = 1.0
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> ; Do not generate velocities
> gen_vel                  = no
> ; options for bonds
> constraints              = none  ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Constrain the starting configuration
> ; since we are continuing from NPT
> continuation             = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 12
> 
> 
> Thank you very much,
> 
> Sonia Aguilera
> PhD student
> ENSCM
>> ; Run control
>> integrator               = sd       ; Langevin dynamics
>> tinit                    = 0
>> dt                       = 0.0005
>> nsteps                   = 40000000   ; 20 ns
>> nstcomm                  = 100
>> ; Neighborsearching and short-range nonbonded interactions
>> cutoff-scheme            = verlet
>> nstlist                  = 20
>> ns_type                  = grid
>> pbc                      = xyz
>> rlist                    = 1.2
>> ; Electrostatics
>> coulombtype              = PME
>> rcoulomb                 = 1.2
>> ; van der Waals
>> vdwtype                  = cutoff
>> vdw-modifier             = potential-switch
>> rvdw-switch              = 1.0
>> rvdw                     = 1.2
>> ; Apply long range dispersion corrections for Energy and Pressure
>> DispCorr                  = EnerPres
> 
> CHARMM uses a force switch, and only apply dispersion correction in the case of
> lipid monolayers.
> 
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
> 
> -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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