[gmx-users] solvation free energy
Justin Lemkul
jalemkul at vt.edu
Fri Jul 17 13:55:24 CEST 2015
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.
>>>>>>
>>>>>
>>>>> --
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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
>>
>> ==================================================
>>
>> --
>> 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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