[gmx-users] SDS micelle
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Mon Nov 22 12:16:42 CET 2004
On Monday 22 November 2004 11:38, Aina Quintilla wrote:
> Dear gromacs users,
>
> I am trying to simulate a micelle of SDS in water.
> my simulation is crashing after some picoseconds ... there are LINCS
> warnings and then the system is blowing apart
try search function of mailing list http://www.gromacs.org/search/index.php
there are several threads, howto correct this
>
> the topology for 1 ds molecule i made:
>
> #include "ffG43a1.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> 1 S 1 SDS S1 1 1.284 32.06 ;
> qtot 1.284
> 2 O 1 SDS O1 1 -0.654 15.9994 ;
> qtot 0.63
> 3 O 1 SDS O12 1 -0.654 15.9994 ;
> qtot -0.024
> 4 OM 1 SDS OH 1 -0.459 15.9994 ;
> qtot -0.483
> 5 OM 1 SDS O13 1 -0.654 15.9994 ;
> qtot -1.137
> 6 CH2 1 SDS C1 1 0.137 14.027 ;
> qtot -1
> 7 CH2 1 SDS C2 1 0 14.027 ;
> qtot -1
> 8 CH2 1 SDS C3 1 0 14.027 ;
> qtot -1
> 9 CH2 1 SDS C4 1 0 14.027 ;
> qtot -1
> 10 CH2 1 SDS C5 1 0 14.027 ;
> qtot -1
> 11 CH2 1 SDS C6 1 0 14.027 ;
> qtot -1
> 12 CH2 1 SDS C7 1 0 14.027 ;
> qtot -1
> 13 CH2 1 SDS C8 1 0 14.027 ;
> qtot -1
> 14 CH2 1 SDS C9 1 0 14.027 ;
> qtot -1
> 15 CH2 1 SDS C10 1 0 14.027 ;
> qtot -1
> 16 CH2 1 SDS C11 1 0 14.027 ;
> qtot -1
> 17 CH3 1 SDS C12 1 0 15.035 ;
> qtot -1
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 2 gb_24
> 1 3 2 gb_24
> 1 4 2 gb_24
> 1 5 2 gb_24
> 4 6 2 gb_18
> 6 7 2 gb_26
> 7 8 2 gb_26
> 8 9 2 gb_26
> 9 10 2 gb_26
> 10 11 2 gb_26
> 11 12 2 gb_26
> 12 13 2 gb_26
> 13 14 2 gb_26
> 14 15 2 gb_26
> 15 16 2 gb_26
> 16 17 2 gb_26
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 7 1
> 2 6 1
> 3 6 1
> 4 8 1
> 5 6 1
> 6 9 1
> 7 10 1
> 8 11 1
> 9 12 1
> 10 13 1
> 11 14 1
> 12 15 1
> 13 16 1
> 14 17 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2
> c3
> 2 1 3 2 ga_28
> 2 1 4 2 ga_28
> 2 1 5 2 ga_28
> 3 1 4 2 ga_28
> 3 1 5 2 ga_28
> 4 1 5 2 ga_28
> 1 4 6 2 ga_25
> 4 6 7 2 ga_29
> 6 7 8 2 ga_12
> 7 8 9 2 ga_12
> 8 9 10 2 ga_12
> 9 10 11 2 ga_12
> 10 11 12 2 ga_12
> 11 12 13 2 ga_12
> 12 13 14 2 ga_12
> 13 14 15 2 ga_12
> 14 15 16 2 ga_12
> 15 16 17 2 ga_12
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3 c4 c5
> 2 1 4 6 1 gd_11
> 1 4 6 7 1 gd_12
> 4 6 7 8 1 gd_17
> 6 7 8 9 1 gd_17
> 7 8 9 10 1 gd_17
> 8 9 10 11 1 gd_17
> 9 10 11 12 1 gd_17
> 10 11 12 13 1 gd_17
> 11 12 13 14 1 gd_17
> 12 13 14 15 1 gd_17
> 13 14 15 16 1 gd_17
> 14 15 16 17 1 gd_17
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> DS
>
> [ molecules ]
> ; Compound #mols
> Protein 1
>
>
> and the parameters that i use to run a simulation, after a long energy
> minimization:
>
>
> constraints = all-bonds
> integrator = md
> dt = 0.0005 ; ps !
> nsteps = 20000
> nstcomm = 1
> nstxout = 10
> nstvout = 1000
> nstfout = 10
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> coulombtype = PME
> rlist = 0.9
> rcoulomb = 1.4
> rvdw = 1.4
> fourierspacing = 0.12
> pme_order = 4
> ewald_rtol = 1e-5
> Tcoupl = berendsen
> tau_t = 0.1
> tc-grps = system
> ref_t = 100
> gen_vel = yes
> gen_temp = 100
> gen_seed = 173529
>
>
> could you please tell me if there is something wrong? i would be very very
> thankfull to any suggestion!
>
Greetings,
Florian
--
-------------------------------------------------------------------------------
Florian Haberl Universitaet Erlangen/
Computer-Chemie-Centrum Nuernberg
Naegelsbachstr. 25
D-91052 Erlangen
Mailto: florian.haberl AT chemie.uni-erlangen.de
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