[gmx-users] Segmentation fault while using external water model
Mark Abraham
mark.j.abraham at gmail.com
Fri Feb 19 02:21:22 CET 2016
Hi,
Are these bonds being converted to constraints, like the original message
suggested?
Mark
On Fri, 19 Feb 2016 02:14 Irem Altan <irem.altan at duke.edu> wrote:
> Hi,
>
> I am still having trouble using TIP4P2005. When I start running my MD
> simulation, it “runs” for a minute or so (although it does not start the
> simulation itself), and then crashes with a segmentation fault.
>
> I have (modified) copy of the amber99sb forcefields in my working
> directory, and I have made the following changes:
>
> - added a tip4p2005.itp file with the correct parameters
> — named OW as OW_tip4p2005 and HW as HW_tip4p2005
> - added the LJ parameters to ffnonbonded.itp:
> OW_tip4p2005 8 16.00 0.0000 A 3.15890e-01 7.74908e-01
> HW_tip4p2005 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
> - added the new atom types to atomtypes.atp:
> HW_tip4p2005 1.00080 ; tip4p/2005 HW
> OW_tip4p2005 16.00000 ; tip4p/2005 OW
> - added the following line to watermodels.dat
> tip4p2005 TIP4P/2005 tip4p/2005
>
> My system consists of a protein in its unit cell, unstripped of its
> crystal waters. Below is how my topology file looks like (after solvation,
> adding ions, and energy minimization):
>
> ; Include forcefield parameters
> #include "./amber99sb.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Other_chain_A2.itp"
> #include "topol_Other_chain_B2.itp"
>
> ; Include water topology
> #include "./amber99sb.ff/tip4p2005.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "./amber99sb.ff/ions.itp"
> #include "./tip4p2005cw.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> Other_chain_A2 1
> Other_chain_B2 1
> HO4 96
> HO4 62
> SOL 5763
> NA 6
> CL 10
>
> where tip4p2005cw.itp is the same file, only with [settles] removed, and
> molname changed to HO4 for labeling purposes.
>
> What could be the problem? (PS, see below for the contents of
> tip4p2005.itp and tip4p2005cw.itp)
>
> Best,
> Irem
>
>
> =======================================================================================================
> tip4p2005.itp (taken from here and slightly modified:
> https://github.com/wesbarnett/trappeua/blob/master/trappeua.ff/tip4p2005.itp
> )
> ————————
>
> TIP4P/2005 Water Model
>
> ; J. L. F. Abascal and C. Vega, J. Chem. Phys 123 234505 (2005)
> ; http://dx.doi.org/10.1063/1.2121687
>
>
> [ moleculetype ]
> ; molname nrexcl
> SOL 2
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 OW_tip4p2005 1 SOL OW 1 0.0000 15.994
> 2 HW_tip4p2005 1 SOL HW1 1 0.5564 1.008
> 3 HW_tip4p2005 1 SOL HW2 1 0.5564 1.008
> 4 MW 1 SOL MW 1 -1.1128 0.0
>
> #ifndef FLEXIBLE
> [ settles ]
> ; i funct doh dhh
> 1 1 0.09572 0.15139
> #else
> [ bonds ]
> ; i j funct length force.c.
> 1 2 1 0.09572 502416.0
> 1 3 1 0.09572 502416.0
>
> [ angles ]
> ; i j k funct angle force.c.
> 2 1 3 1 104.52 628.02
> #endif
>
> [ exclusions ]
> 1 2 3 4
> 2 1 3 4
> 3 1 2 4
> 4 1 2 3
>
> ; The position of the dummy is computed as follows:
> ;
> ; O
> ;
> ; D
> ;
> ; H H
> ;
> ; a = b = (1/2) * (distance(OD) / [ cos (angle(DOH)) * distance(OH) ] )
> ; = (1/2) * (0.01546 nm / [ cos (52.26 deg) * 0.09572 nm ] )
> ; = 0.13193828
> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>
> [ virtual_sites3 ]
> ; Vsite from funct a b
> 4 1 2 3 1 0.13193828 0.13193828
>
>
> ==============
> tip4p2005cw.itp
> ————————
>
> ; TIP4P/2005 Water Model
>
> ; J. L. F. Abascal and C. Vega, J. Chem. Phys 123 234505 (2005)
> ; http://dx.doi.org/10.1063/1.2121687
>
>
> [ moleculetype ]
> ; molname nrexcl
> HO4 2
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 OW_tip4p2005 1 SOL OW 1 0.0000 15.994
> 2 HW_tip4p2005 1 SOL HW1 1 0.5564 1.008
> 3 HW_tip4p2005 1 SOL HW2 1 0.5564 1.008
> 4 MW 1 SOL MW 1 -1.1128 0.0
>
> ;#ifndef FLEXIBLE
> ;[ settles ]
> ; i funct doh dhh
> ; 1 1 0.09572 0.15139
> ;#else
> [ bonds ]
> ; i j funct length force.c.
> 1 2 1 0.09572 502416.0
> 1 3 1 0.09572 502416.0
>
> [ angles ]
> ; i j k funct angle force.c.
> 2 1 3 1 104.52 628.02
> ;#endif
>
> [ exclusions ]
> 1 2 3 4
> 2 1 3 4
> 3 1 2 4
> 4 1 2 3
>
> ; The position of the dummy is computed as follows:
> ;
> ; O
> ;
> ; D
> ;
> ; H H
> ;
> ; a = b = (1/2) * (distance(OD) / [ cos (angle(DOH)) * distance(OH) ] )
> ; = (1/2) * (0.01546 nm / [ cos (52.26 deg) * 0.09572 nm ] )
> ; = 0.13193828
> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>
> [ virtual_sites3 ]
> ; Vsite from funct a b
> 4 1 2 3 1 0.13193828 0.13193828
>
> --
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