[gmx-users] Martini with PME, temp two low

[Justin Lemkul]

On 4/25/13 10:05 AM, Dr. Vitaly Chaban wrote:
> PME should NOT be used with charged systems, for obvious reasons.
>
>

FYI Gromacs provides a neutralizing background charge.

http://comments.gmane.org/gmane.science.biology.gromacs.user/639

There may, of course, be issues with the physical reality of such a setup, but 
this is a common question.

-Justin

> On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950
> <Stephane.ABEL at cea.fr>wrote:
>
>> And ? sorry but i do not understand...
>>
>> Stephane
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 25 Apr 2013 15:39:12 +0200
>> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
>> Subject: Re: [gmx-users] Martini with PME, temp two low
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID:
>>          <CAPXdD+bDiuQWG_3eWZ_0yb=
>> AyNLaAF08vt46uSEL4wk_BJgbeg at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hmmm....
>>
>> Aren't the keywords here "charged system" + "PME"?
>>
>>
>> Dr. Vitaly Chaban
>>
>>
>>
>> On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole <x.periole at rug.nl> wrote:
>>
>>>
>>> Did you visualise the system? T in function of time? Epot in function of
>>> time?
>>>
>>> As a side note (not relevant for PME) the mix of nstlist = 10 and the
>>> rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
>>> rlist=1.4 if nstlist =10.
>>>
>>> On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
>>> wrote:
>>>
>>>> Hello all,
>>>>
>>>> I am trying to test the martini force field with PME for a charged
>>> system that contains na+, water, surfactant, octane molecules at 298K and
>>> P=0.1MPa. My system works well, if i use the standard shift parameters
>>> (correct temp, and pressure). But for for the simulation with PME , the
>>> temp of the system decrease to  290 K. Below my *.mdp parameters for a
>> NPT
>>> equil at 298K
>>>>
>>>>
>>>> integrator               = md
>>>> dt                       = 0.020
>>>> nsteps                   = 10000 ; 200ps
>>>> nstcomm                  = 10
>>>> comm-grps        =
>>>> ;refcoord_scaling         = com
>>>>
>>>> nstxout                  = 0
>>>> nstvout                  = 0
>>>> nstfout                  = 0
>>>> nstlog                   = 1000
>>>> nstenergy                = 100
>>>> ;nstxtcout                = 1000
>>>> xtc_precision            = 100
>>>> ;xtc-grps                 =
>>>> energygrps               = AOT W ION OCT
>>>>
>>>> nstlist                  = 10
>>>> ns_type                  = grid
>>>> pbc                      = xyz
>>>> rlist                    = 1.
>>>>
>>>> ; PME parameters
>>>> coulombtype              = PME
>>>> rcoulomb                 = 1.2
>>>> rvdw                     = 1.2
>>>> fourierspacing           = 0.12
>>>> fourier_nx               = 0
>>>> fourier_ny               = 0
>>>> fourier_nz               = 0
>>>> pme_order                = 4
>>>>
>>>> tcoupl                   = v-rescale
>>>> tc-grps                  = AOT_W_ION OCT
>>>> tau_t                    = 1.0 1.0
>>>> ref_t                    = 298 298
>>>> Pcoupl                   = berendsen
>>>> Pcoupltype               = isotropic
>>>> tau_p                    = 1.0
>>>> compressibility          = 4.5e-5
>>>> ref_p                    = 1.0
>>>>
>>>> ;gen_vel                  = no
>>>> ;gen_temp                 = 0
>>>> ;gen_seed                 = 473529
>>>>
>>>>
>>>> ; MARTINI and CONSTRAINTS
>>>> ; for ring systems and stiff bonds constraints are defined
>>>> ; which are best handled using Lincs.
>>>>
>>>> constraints              = none
>>>> constraint_algorithm     = Lincs
>>>> unconstrained_start      = no
>>>> lincs_order              = 4
>>>> lincs_warnangle          = 3
>>>>
>>>>
>>>> Results obtained with W/ PME
>>>>
>>>>    Statistics over 10001 steps using 1001 frames
>>>>
>>>>    Energies (kJ/mol)
>>>>            Bond       G96Angle        LJ (SR)   Coulomb (SR)   Coul.
>>> recip.
>>>>     1.63789e+04    1.25195e+03   -4.02093e+05   -8.22079e+03
>>> -4.86843e+04
>>>>       Potential    Kinetic En.   Total Energy    Temperature Pressure
>>> (bar)
>>>>    -4.41367e+05    7.81801e+04   -3.63187e+05    2.90373e+02
>>> -1.76470e+01
>>>>     T-AOT_W_ION          T-OCT
>>>>     2.90629e+02    2.90357e+02
>>>>
>>>> Results W:o PME
>>>>
>>>>    Energies (kJ/mol)
>>>>            Bond       G96Angle        LJ (SR)   Coulomb (SR)
>>>   Potential
>>>>     1.60482e+04    1.24820e+03   -3.34608e+05   -7.33665e+02
>>> -3.18046e+05
>>>>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>>>>     8.02685e+04   -2.37777e+05    2.98129e+02   -3.07123e+01
>>>>
>>>>           Box-X          Box-Y          Box-Z
>>>>     1.52926e+01    1.52926e+01    1.52926e+01
>>>>
>>>>
>>>>     T-AOT_W_ION          T-OCT
>>>>     2.98141e+02    2.98129e+02
>>>>
>>>>
>>>> Did I miss something ?
>>>>
>>>>
>>>> Note that for the moment i do not use the polarizable water model.
>>>>
>>>> Thanks for your help
>>>>
>>>> Stephane
>>>>
>>>>
>>>>
>>
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================