[gmx-users] Gromos 53a6, .mdp parameters for reaction field
V.V.Chaban
vvchaban at gmail.com
Tue Jul 21 22:34:59 CEST 2015
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 ...*
>> > --
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>
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> Rewards work better than punishment ...
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