[gmx-users] Gromos 53a6, .mdp parameters for reaction field
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Mon Aug 10 18:00:17 CEST 2015
As an update,
After reading the suggested links I tried two .mdp files which were
suggested in discussions as solutions. Both worked without any problem on
my system.
1) rlist/r(columb/vdw)=(1.4/1.4) , in fact the problem seems to be the
"twin-range + RF"
2) I used "twin-range + RF" BUT I reduced the nstlist to 1, this also works
for my system.
Thanks for your comments.
Cheers
Mohsen
On Tue, Jul 21, 2015 at 4:44 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:
> I looked at the first link, it was a useful discussion.
> Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and
> everything is working properly till now.
> It seems the problem was the "twin-range" + RF with this version of
> Gromacs as has been discussed and you mentioned already.
>
> I am playing a little bit to see if I everything will be fine with the
> rest of test simulation.
> I will reply again after my tests.
>
> Thanks for the links
>
> Cheers
> Mohsen
>
> On Tue, Jul 21, 2015 at 4:21 PM, João M. Damas <jmdamas at itqb.unl.pt>
> wrote:
>
>> I really think you may be losing time with LINCS parameters. Look at these
>> links too:
>>
>>
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html
>> http://redmine.gromacs.org/issues/1400
>>
>> You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really
>> think that this may be the source of your problems. The links that I sent
>> you present solutions to your problem, but almost always at a
>> computational
>> cost, i.e. slower simulations.
>>
>> João
>>
>>
>> On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban <vvchaban at gmail.com> wrote:
>>
>> > Maybe indeed downgrade to an earlier version.
>> >
>> > I, for sure, successfully used reaction field with gromacs 3-3-3
>> > (imagine when it was).
>> >
>> > Professor Vitaly V. Chaban
>> >
>> >
>> >
>> >
>> > On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour
>> > <ramezanpour.mohsen at gmail.com> wrote:
>> > > Hi Chaban,
>> > >
>> > > Me too, but I do not know why starting with the same initial
>> structures
>> > and
>> > > also starting from equilibrated structures again cause LINCS problems
>> in
>> > one
>> > > not in the other one.
>> > >
>> > > I have tried lincs-iter and lincs-order and also lincs allowable angle
>> > > deviations but LINCS error still exist. This is why I think there is
>> > > something wrong with other parameters, e.g. reaction field!
>> > > Sure, I will look at epsilon_r, thanks.
>> > >
>> > >
>> > > On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban <vvchaban at gmail.com>
>> wrote:
>> > >>
>> > >> I do not see much connection between bond constraints and treatment
>> of
>> > >> electrostatics beyond the cut-off distance.
>> > >>
>> > >> There is also an "epsilon_r" keyword. I would investigate what
>> exactly
>> > >> it means and whether it is used in the reaction field procedure.
>> > >>
>> > >> The "all-bonds" contraint often results in different problems. You
>> > >> will have to play with the relevant parameters, like lincs_order and
>> > >> allowable deviation.
>> > >>
>> > >>
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour
>> > >> <ramezanpour.mohsen at gmail.com> wrote:
>> > >> > Dear Gromacs users,
>> > >> >
>> > >> > I am interested in simulation of lipid bilayers with Gromos96 53a6.
>> > >> > As I understood this force field has been parametrized with
>> reaction
>> > >> > field
>> > >> > instead of pme.
>> > >> >
>> > >> > Based on literatures, I have the following .mdp parameters:
>> > >> > But I am not sure of those as my system has lots of LINCS warnings
>> > with
>> > >> > these parameters.
>> > >> >
>> > >> > integrator = md
>> > >> > tinit = 0
>> > >> > dt = 0.002
>> > >> > nsteps = 50000
>> > >> > nstcomm = 1
>> > >> > comm-grps =
>> > >> >
>> > >> >
>> > >> > nstxout = 0
>> > >> > nstvout = 0
>> > >> > nstfout = 0
>> > >> > nstenergy = 100
>> > >> > nstxtcout = 5000
>> > >> > xtc-precision = 1000
>> > >> > energygrps = system
>> > >> >
>> > >> > nstlist = 5
>> > >> > ns_type = grid
>> > >> > pbc = xyz
>> > >> > rlist = 0.8
>> > >> >
>> > >> > coulombtype = reaction_field
>> > >> > rcoulomb-switch = 0
>> > >> > rcoulomb = 1.4
>> > >> > epsilon_rf = 62
>> > >> > vdw-type = Cut-off
>> > >> > rvdw-switch = 0
>> > >> > rvdw = 1.4
>> > >> > DispCorr = no
>> > >> >
>> > >> >
>> > >> > tcoupl = v-rescale
>> > >> > tc_grps = lipid water_ion
>> > >> > tau_t = 0.1 0.1
>> > >> > ref_t = 353 353
>> > >> > Pcoupl = berendsen
>> > >> > pcoupltype = semiisotropic
>> > >> > tau_p = 1.0 1.0
>> > >> > compressibility = 4.6e-5 4.6e-5
>> > >> > ref_p = 1.0 1.0
>> > >> >
>> > >> >
>> > >> > gen_vel = yes
>> > >> > gen_temp = 353
>> > >> > gen_seed = 17352
>> > >> >
>> > >> > constraints = all-bonds
>> > >> > constraint-algorithm = Lincs
>> > >> > unconstrained-start = no
>> > >> > shake-tol = 1e-04
>> > >> > morse = no
>> > >> >
>> > >> >
>> > >> > Interestingly, when I use common Gromos parameters including pme,
>> as
>> > >> > follows, I do not have any LINCS problem with my system.
>> > >> >
>> > >> > integrator = md
>> > >> > tinit = 0
>> > >> > dt = 0.002
>> > >> > nsteps = 50000
>> > >> > pbc = xyz
>> > >> > comm-mode = linear
>> > >> > nstcomm = 1
>> > >> > comm-grps = system
>> > >> >
>> > >> >
>> > >> > nstxout = 0
>> > >> > nstvout = 0
>> > >> > nstfout = 0
>> > >> > nstlist = 10
>> > >> > ns_type = grid
>> > >> > nstenergy = 100
>> > >> > nstxtcout = 5000
>> > >> > energygrps = system
>> > >> >
>> > >> >
>> > >> > coulombtype = pme
>> > >> > rcoulomb = 1.0
>> > >> > rlist = 1.0
>> > >> > vdw-type = cutoff
>> > >> > rvdw = 1.0
>> > >> > DispCorr = no
>> > >> > table-extension = 1
>> > >> >
>> > >> >
>> > >> > tcoupl = v-rescale
>> > >> > tc-grps = lipid water_ion
>> > >> > tau-t = 0.1 0.1
>> > >> > ref-t = 353 353
>> > >> > Pcoupl = berendsen
>> > >> > Pcoupltype = semiisotropic
>> > >> > ref-p = 1.0 1.0
>> > >> > tau-p = 1.0 1.0
>> > >> > compressibility = 4.5e-5 4.5e-5
>> > >> >
>> > >> >
>> > >> > constraints = all-bonds
>> > >> > constraint-algorithm = Lincs
>> > >> >
>> > >> >
>> > >> > gen_vel = yes
>> > >> > gen_temp = 353
>> > >> > gen_seed = -1
>> > >> >
>> > >> >
>> > >> > Since the initial structures are the same, I think my parameters
>> for
>> > >> > reaction field one has problem. I have also tried shorter time
>> steps
>> > >> > (even
>> > >> > 0.5 fs) and also started from different initial structures but the
>> > >> > problem
>> > >> > still exist.
>> > >> >
>> > >> > I searched the mailing list but I could not find my answer
>> completely.
>> > >> > Please let me know if you have any idea about parameters or if you
>> > have
>> > >> > any
>> > >> > .mdp file for reaction field (Gromos 53a6).
>> > >> >
>> > >> > Cheers
>> > >> > Mohsen
>> > >> > --
>> > >> > *Rewards work better than punishment ...*
>> > >> > --
>> > >> > Gromacs Users mailing list
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>> > >
>> > >
>> > > --
>> > > Rewards work better than punishment ...
>> > --
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>>
>>
>> --
>> João M. Damas
>> PhD Student
>> Protein Modelling Group
>> ITQB-UNL, Oeiras, Portugal
>> Tel:+351-214469613
>> --
>> Gromacs Users mailing list
>>
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>
>
>
> --
> *Rewards work better than punishment ...*
>
--
*Rewards work better than punishment ...*
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