[gmx-users] Perturbation Thermodynamic Integration

Justin Lemkul jalemkul at vt.edu
Tue May 16 16:00:39 CEST 2017



On 5/16/17 9:53 AM, Dan Gil wrote:
> Hi,
>
> The latest version of Gromacs I have is 5.1. Using this version, grompp
> produces no warnings or errors.
>
> I am using OPLS-AA, and I didn't have any issues with it thus far. I
> inherited this research project though 3 years ago. Is there something you
> think I should look at with scrutiny?
>

The rvdw is very long (no FF uses one like that) though cutoffs for OPLS-AA vary 
paper by paper, unfortunately.  Typical values for all cutoffs are 1.0.  Your 
fourierspacing is about 3-4 times too large so your use of PME is probably 
insufficiently accurate.  Stick with the default of 0.12 to get beta ~0.34 or so.

-Justin

> On Tue, May 16, 2017 at 9:42 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Yes that looks like it is the envelope of the new warning. What does grompp
>> from 2016.3 report?
>>
>> (Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd
>> reject that method immediately unless there was evidence that it worked
>> well for a range of observables, and was consistent with other practice for
>> that force field. If there is such evidence, for my information, what model
>> / force field does it like that?)
>>
>> Mark
>>
>> On Tue, May 16, 2017 at 3:30 PM Dan Gil <dan.gil9973 at gmail.com> wrote:
>>
>>> Sorry, here is the mdp file:
>>>
>>> ;Integration Method and Parameters
>>> integrator               = sd
>>> nsteps                   = 100000
>>> dt = 0.002
>>> nstenergy                = 1000
>>> nstlog                   = 5000
>>>
>>> ;Output Control
>>> nstxout = 0
>>> nstvout = 0
>>>
>>> ;Cutoff Schemes
>>> cutoff-scheme            = group
>>> rlist                    = 1.0
>>> vdw-type                 = cut-off
>>> rvdw                     = 2.0
>>>
>>> ;Coulomb interactions
>>> coulombtype              = pme
>>> rcoulomb                 = 1.0
>>> fourierspacing           = 0.4
>>>
>>> ;Constraints
>>> constraints              = all-bonds
>>>
>>> ;Temperature coupling
>>> tcoupl                   = v-rescale
>>> tc-grps                  = system
>>> tau-t                    = 0.1
>>> ref-t                    = 300
>>>
>>> ;Pressure coupling
>>> pcoupl = parrinello-rahman
>>> ref-p = 1.01325
>>> compressibility = 4.5e-5
>>> tau-p = 5
>>>
>>> ;Free energy calculation
>>> free-energy              = yes
>>> init-lambda-state        = 8
>>> delta-lambda             = 0
>>> fep-lambdas              =
>>> calc-lambda-neighbors    = 1
>>> vdw_lambdas              = 0 0   0   0   0   0   0   0   0   0   0
>>> coul_lambdas             = 0 0   0   0   0   0   0   0   0   0   0
>>> bonded_lambdas           = 0 0   0   0   0   0   0   0   0   0   0
>>> restraint_lambdas        = 0 0   0   0   0   0   0   0   0   0   0
>>> mass_lambdas             = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
>>> couple-moltype           = HEPT
>>> couple-lambda0           = vdwq
>>> couple-lambda1           = none
>>> couple-intramol          = no
>>> nstdhdl                  = 10
>>>
>>>
>>> On Tue, May 16, 2017 at 1:02 AM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> What use are you making of constraints? Justin suggested sharing a full
>>> mdp
>>>> file, which I think may help. We discovered last year that you can get
>>>> equipartition failure for (IIRC) all-bonds constraints for moieties
>> like
>>>> -CH2Cl, and latest grompp now detects this.
>>>>
>>>> Mark
>>>>
>>>> On Tue, 16 May 2017 01:16 Dan Gil <dan.gil9973 at gmail.com> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> The last thread was getting too big, and the conversation evolved to
>> a
>>>>> topic different from my original question, so I decided to start a
>> new
>>>>> thread.
>>>>>
>>>>> We were discussing thermodynamic integration, and why the
>> mass_lambdas
>>>>> would have any contribution to the derivative of the Hamiltonian.
>>>>>
>>>>> I found a source (link below) which derives the Gibbs free energy
>>> change
>>>> as
>>>>> a function of lambda. I learned that the mass contribution is often
>>>> assumed
>>>>> to be small and negligible, given that the mass difference between
>> the
>>>> two
>>>>> lambda states are small.
>>>>> http://www.tandfonline.com/doi/abs/10.1080/00268970600893060
>>>>>
>>>>> I think that the mass of the two lambda states that equation (14) is
>>>>> referring to is the total mass (mass of solvent plus solute). My
>> system
>>>> is
>>>>> 1 solute (~40 atoms) infinitely diluted in solvent (23500). I wonder
>>> if I
>>>>> am getting nonzero mass contributions (in my dhdl.xvg output) because
>>> of
>>>>> finite-size effects? Would completely neglecting the mass
>> contributions
>>>> be
>>>>> acceptable? Does doing this technically change the system to one that
>>> is
>>>> 1
>>>>> solute and an infinite number of solvent molecules where the mass
>>>>> contributions limit is zero?
>>>>>
>>>>> Best Regards,
>>>>>
>>>>> Dan
>>>>> --
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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 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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