[gmx-users] Turning off electrostatics between protein and water, then protein and protein
Justin Lemkul
jalemkul at vt.edu
Sun Nov 19 22:26:51 CET 2017
On 11/19/17 3:42 PM, Mark Abraham wrote:
> Hi,
>
> Oh, I see. Yes that feature turns off both kinds of non-bonded
> interactions. Then there is nothing useful for what you want.
Couldn't this be done with the free energy code?
Turn off protein-water electrostatics by running in the lambda=1 state with:
couple-lambda0 = vdw-q
couple-lambda1 = vdw
couple-intramol = no
Then switch to couple-intramol = yes to turn off protein-protein
interactions.
I imagine it would be a huge memory hog and would run really slowly, but
it's a possible solution.
-Justin
> Mark
>
> On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan <davtyan.aram at gmail.com> wrote:
>
>> Hi Mark,
>>
>> I apologize if I did not describe my problem correctly the first time, but
>> I need the VdW interactions to stay on between all atoms at all times. I
>> only need to turn off the electrostatic interactions between water and
>> proteins.
>>
>> Thanks,
>>
>> Aram
>>
>> Hi,
>>> You've described the feature correctly. Whether it is useful in a study
>>> design is another matter :-)
>>>
>>> Mark
>>>
>>> On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan <davtyan.aram at gmail.com>
>>> wrote:
>>>
>>>> Hi Mark,
>>>>
>>>> I am not sure I understood. If I for example say "energygrp-excl =
>>> Protein
>>>> Water" would not I turn off all the non-bonded interactions between
>> water
>>>> and protein? Or did you mean something else?
>>>>
>>>> Thanks,
>>>>
>>>> Aram
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> In the group scheme you can turn on energy-group exclusions to get
>> this
>>>>> working, but of course all of those states are sampling unphysical
>>> things
>>>>> from a broken forcefield. That can be OK, but you will have to be
>> able
>>> to
>>>>> defend that claim.
>>>>>
>>>>> Mark
>>>>>
>>>>> On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan <davtyan.aram at gmail.com
>>>>> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am running simulations of two protein domains in tip4p water and
>>>> 0.15M
>>>>>> salt concentration that contain up to 650,000 atoms total. The
>>> protein
>>>>>> domains are separated from each other at the start of each
>> simulation
>>>>> and I
>>>>>> am measuring how the distance between them changes over time.
>>>>>>
>>>>>> Now, I need to do the same simulations, but with electrostatics
>>> between
>>>>>> proteins and water turned off (with water-water, protein-protein,
>>>>>> ion-water, ion-protein electrostatics remaining). Then I need to
>>> repeat
>>>>>> that, but additionally turning off electrostatics between the two
>>>>> domains.
>>>>>> Water-water, ion-water, ion-protein, intra-domain electrostatics
>>> should
>>>>>> remain on.
>>>>>>
>>>>>> What will be the best way to do this?
>>>>>>
>>>>>> I am using CHARMM27 force field and the following settings to run
>> the
>>>>>> production simulations:
>>>>>>
>>>>>> integrator = md
>>>>>> dt = 0.002
>>>>>> nsteps = 1000000 ; 2ns
>>>>>> nstlog = 1000
>>>>>> nstxout = 5000
>>>>>> nstvout = 5000
>>>>>> nstfout = 5000
>>>>>> nstcalcenergy = 100
>>>>>> nstenergy = 1000
>>>>>> ;
>>>>>> cutoff-scheme = Verlet
>>>>>> nstlist = 20
>>>>>> rlist = 1.2
>>>>>> coulombtype = pme
>>>>>> rcoulomb = 1.2
>>>>>> vdwtype = Cut-off
>>>>>> vdw-modifier = Force-switch
>>>>>> rvdw_switch = 1.0
>>>>>> rvdw = 1.2
>>>>>> ;
>>>>>> tcoupl = Nose-Hoover
>>>>>> tc_grps = Protein Non-Protein
>>>>>> tau_t = 1.0 1.0
>>>>>> ref_t = 300.0 300.0
>>>>>> ;
>>>>>> pcoupl = Parrinello-Rahman
>>>>>> pcoupltype = isotropic
>>>>>> tau_p = 5.0
>>>>>> compressibility = 4.5e-5
>>>>>> ref_p = 1.0
>>>>>> ;
>>>>>> constraints = h-bonds
>>>>>> constraint_algorithm = LINCS
>>>>>> continuation = yes
>>>>>> ;
>>>>>> nstcomm = 100
>>>>>> comm_mode = linear
>>>>>> comm_grps = Protein Non-Protein
>>>>>> ;
>>>>>> refcoord_scaling = com
>>>>>>
>>>>>>
>>>>>> I have tried to use the energy groups (energygrp-table) to specify
>>>>>> interaction tables between water and protein, where I would set the
>>>>>> electrostatic potential to zero. However, given that
>> energygrp-table
>>>> and
>>>>>> Varlet cutoff-scheme are incompatible, I could not make it work.
>> But
>>> it
>>>>> is
>>>>>> possible that I did something wrong.
>>>>>>
>>>>>> Thank you in advance,
>>>>>>
>>>>>> Aram
>>>>>> --
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>>
>>
>> --
>> Aram Davtyan, Ph.D.
>> Center for Theoretical Biological Physics
>> Rice University
>> E-mail: adavtyan at rice.edu <adavtyan at uchicago.edu>
>> Phone: (919)265-8369
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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