[gmx-users] Virtual site and constraints

[David van der Spoel]

Нилов Дмитрий wrote:
> Hello!
> I would like to involve formate molecule (HCOO-)in my dynamics, but I have the problem when I use virtual site (type 3fd)for it.
> 
> When I run grompp for single formate molecule, it`s ok.
> But after solvating in bath of solvent (tip3p) grompp runs with error:

In this case you would be best off defining three constraints from
H O1
H O2
O1 O2
and define the carbon as a virtual site defined by the plane (check 
TIP4P topology).

> 
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removed      1     Proper Dih.s with virtual sites,     0 left
> Converted    1      Constraints with virtual sites to connections,     2 left
> ERROR: Cannot have constraint (5-1) with virtual site (1)
> ERROR: Cannot have constraint (8-1) with virtual site (1)
> ERROR: Cannot have constraint (11-1) with virtual site (1)
> ERROR: Cannot have constraint (14-1) with virtual site (1)
> ..........................................
> ERROR: Cannot have constraint (3101-1) with virtual site (1)
> ERROR: Cannot have constraint (3104-1) with virtual site (1)
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: vsite_parm.c, line: 686
> 
> Fatal error:
> There were 1034 virtual sites involved in constraints
> -------------------------------------------------------
> 
> And 1034 is number of water molecules. In my mdp file the line that corresponds to constraints is
> "constraints = none". This is my topology:
> 
> #include "ffoplsaa.itp"
> 
> [ moleculetype ]
> ; Name            nrexcl
> FMT                 3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
>      1   opls_279      1    FMT      H      1       0.22          0   ; qtot 0.22
>      2   opls_271      1    FMT      C      1       0.58     13.019   ; qtot 0.8
>      3   opls_272      1    FMT     O1      1       -0.9    15.9994   ; qtot -0.1
>      4   opls_272      1    FMT     O2      1       -0.9    15.9994   ; qtot -1
> 
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1 
>     2     3     1 
>     2     4     1 
> 
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>     1     2     3     1    ang_FMT_H_C_O1
>     1     2     4     1    ang_FMT_H_C_O2
>     3     2     4     1    ang_FMT_O1_C_O2
> 
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2            c3
>     1     3     2     4     1    improper_O_C_X_Y
> 
> [ virtual_sites3 ]
> ;  ai    aj    ak    al funct            c0            c1
>     1     2     3     4     2 
> 
> ; Include water topology
> #include "tip3p.itp"
> 
> [ system ]
> ; Name
> FMT in water
> 
> [ molecules ]
> ; Compound        #mols
> FMT                 1
> SOL              1034
> 
> 
> Could You help me to solve this roblem!
> Thanks!
> _____________
> Dmitri Nilov
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se