[gmx-users] solvation free energy
Daniele Veclani
danieleveclani at gmail.com
Fri Jul 17 13:44:27 CEST 2015
OK! I got it.
I have to put:
couple-intramol = yes
but I have to define couple-lambda 0 and couple-lamba-1?
how do I turn off the 1-4 pair interaction?
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
>
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