[gmx-users] solvation free energy
Daniele Veclani
danieleveclani at gmail.com
Fri Jul 17 17:29:40 CEST 2015
I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ?
I read in the manual (section 5.3.4) that can turn off the 1-4 interactions
without ever touching the topology, by using the couple-moltype,
couple-lambda0, couple-lambda 1, and couple-intramol keywords.
Can I do this?
Best regards
D.V.
2015-07-17 13:55 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 7/17/15 7:44 AM, Daniele Veclani wrote:
>
>> OK! I got it.
>>
>> I have to put:
>> couple-intramol = yes
>>
>> but I have to define couple-lambda 0 and couple-lamba-1?
>>
>>
> Yes, you have to tell mdrun what you're transforming.
>
> how do I turn off the 1-4 pair interaction?
>>
>>
> That requires explicit use of [pairs_nb], as I recall. There was a bug
> fix for that recently, so make sure you're using version 5.0.5.
>
> -Justin
>
>
>
>> 2015-07-17 13:32 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 7/17/15 6:34 AM, Daniele Veclani wrote:
>>>
>>> I read the manual and also some examples of free energy calculation.
>>>>
>>>> when I do the simulation:
>>>> M(vacuo) --> nothing(vacuo)
>>>>
>>>> I leave only intramolecular interactions.
>>>>
>>>> How can I just leave these interactions? I don't find the answer in the
>>>> manual.
>>>>
>>>>
>>>> "couple-intramol = no" does not subject intramolecular interactions to
>>> lambda coupling. But doing this in vacuo is pointless, because then by
>>> definition, nothing changes.
>>>
>>> -Justin
>>>
>>>
>>>
>>> Best regards
>>>> D.V.
>>>>
>>>> 2015-07-17 10:10 GMT+02:00 <hannes.loeffler at stfc.ac.uk>:
>>>>
>>>> I do not know how your top file looks like and what you have done to
>>>> it.
>>>>
>>>>>
>>>>> The setup procedure to create the topolog file would be as for a
>>>>> standard
>>>>> MD simulation with M. You would make sure that the "QUI" label referes
>>>>> to
>>>>> the right indexes in your index file and run TI with you preferred
>>>>> protocol. This simplified setup procedure ensures that you do not have
>>>>> to
>>>>> modify the topology file in any way esp. not to have to set up an
>>>>> explicit
>>>>> B state.
>>>>>
>>>>> I suggest to read all parts relating to couple-* in the manual. This
>>>>> is
>>>>> scattered over several places in the text.
>>>>>
>>>>> Cheers,
>>>>> Hannes.
>>>>>
>>>>> ________________________________________
>>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
>>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of
>>>>> Daniele
>>>>> Veclani [danieleveclani at gmail.com]
>>>>> Sent: 17 July 2015 08:57
>>>>> To: gmx-users at gromacs.org
>>>>> Subject: Re: [gmx-users] solvation free energy
>>>>>
>>>>> Thank you for your answer.
>>>>>
>>>>> I read the manual. As I understand it, I should be deleted, from .top
>>>>> file, the
>>>>> section of non-bonded parameters. It's right?
>>>>>
>>>>> Of course, after the VdW I'll change the electrostatic transformation.
>>>>>
>>>>> Best regards
>>>>> D.V.
>>>>>
>>>>> 2015-07-16 16:55 GMT+02:00 Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk
>>>>> >:
>>>>>
>>>>> The couple-* parameters take already care of including the non-bonded
>>>>>
>>>>>> terms internal to your molecule to correctly describe the transfer of
>>>>>> M
>>>>>> to vacuum. That's the point of those parameters so that you would not
>>>>>> have to run an additional "correction" in vacuo. See the discussion
>>>>>> in
>>>>>> the manual (it's section 5.3 for Gromacs 4.6.x). You would also need
>>>>>> to
>>>>>> compute the electrostatic transformation.
>>>>>>
>>>>>> On Thu, 16 Jul 2015 16:26:44 +0200
>>>>>> Daniele Veclani <danieleveclani at gmail.com> wrote:
>>>>>>
>>>>>> I'm trying to calculate the solvation free energy of a molecule
>>>>>> (M).
>>>>>>
>>>>>>> I have done:
>>>>>>> M+water ---> dum+water
>>>>>>>
>>>>>>> Now I have to do:
>>>>>>> M(vacuo) --> dum(vacuo)
>>>>>>>
>>>>>>> In this case I have a problem, in fact I find a DG = 0.00000 and
>>>>>>> within the .xvg file there are only zeros.
>>>>>>>
>>>>>>> Where is the problem?
>>>>>>>
>>>>>>> I use gromacs 5.0.4 and my .mdp file (for lambda 00) is:
>>>>>>> integrator = sd
>>>>>>> tinit = 0
>>>>>>> dt = 0.002
>>>>>>> nsteps = 2500000
>>>>>>> comm_mode = angular
>>>>>>> nstcomm = 100
>>>>>>> nstxout = 500
>>>>>>> nstvout = 500
>>>>>>> nstfout = 0
>>>>>>> nstlog = 500
>>>>>>> nstenergy = 500
>>>>>>> nstxout-compressed = 0
>>>>>>> cutoff-scheme = group
>>>>>>> nstlist = 0
>>>>>>> ns_type = simple
>>>>>>> pbc = no
>>>>>>> rlist = 0
>>>>>>> coulombtype = cutoff
>>>>>>> rcoulomb = 0
>>>>>>> epsilon_r = 1
>>>>>>> vdwtype = cutoff
>>>>>>> rvdw = 0
>>>>>>> DispCorr = no
>>>>>>> fourierspacing = 0.12
>>>>>>> pme_order = 6
>>>>>>> ewald_rtol = 1e-06
>>>>>>> epsilon_surface = 0
>>>>>>> tcoupl = berendsen
>>>>>>> tc_grps = system
>>>>>>> tau_t = 0.1
>>>>>>> ref_t = 300
>>>>>>> Pcoupl = no
>>>>>>> tau_p = 1.0
>>>>>>> compressibility = 4.5e-05
>>>>>>> ref_p = 1.0
>>>>>>> free_energy = yes
>>>>>>> init_lambda_state = 0
>>>>>>> delta_lambda = 0
>>>>>>> calc_lambda_neighbors = 1
>>>>>>> vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70
>>>>>>> 0.80 0.90 1.00
>>>>>>> coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>>>>>>> 0.00 0.00 0.00
>>>>>>> bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>>>>>>> 0.00 0.00 0.00
>>>>>>> restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>>>>>>> 0.00 0.00 0.00
>>>>>>> mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>>>>>>> 0.00 0.00 0.00
>>>>>>> temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
>>>>>>> 0.00 0.00 0.00
>>>>>>> sc-alpha = 0.5
>>>>>>> sc-coul = no
>>>>>>> sc-power = 1.0
>>>>>>> sc-sigma = 0.3
>>>>>>> couple-moltype = QUI
>>>>>>> couple-lambda0 = vdw
>>>>>>>
>>>>>>> couple-lambda1 = none
>>>>>>> couple-intramol = no
>>>>>>> nstdhdl = 10
>>>>>>> gen_vel = no
>>>>>>> constraints = all-bonds ; we only have C-H bonds here
>>>>>>> constraint-algorithm = lincs
>>>>>>> continuation = no
>>>>>>> lincs-order = 12
>>>>>>>
>>>>>>> Best regards
>>>>>>> Daniele Veclani.
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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>>>>>> --
>>>>>>
>>>>> Gromacs Users mailing list
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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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>>>
> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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