[gmx-users] tabulated dihedral potential

[Mark Abraham]

Hi,

Can't tell, but you should test such things by using mdrun -rerun to write
energies and forces for a trivial input that you can verify by hand (e.g.
four atoms with a single interaction)

Mark

On Tue, Jan 19, 2016 at 6:01 PM Parvez Mh <parvezmh89 at gmail.com> wrote:

> (Repost)
> Dear all:
>
> I am trying to use tabulated dihedral potential in my simulation. As a test
> case, i tried with something known case like octane. I know the
> Ryckaert-Bellemans function coefficient of dihedral. So i tried to create a
> table from this known case using following fortran code
>
> program table
>     implicit none
>     double precision::a0,a1,a2,a3,a4,a5
>     double precision::x
>     double precision::fx,dfx
>     character(len=15)::filename
>     integer::angle_deg
>     a0=8.3945
>     a1=16.7787
>     a2=1.1332
>     a3=-26.3070
>     a4=0.000676
>     a5=-0.00001816
>     filename='table_d0.xvg'
>     open(unit=100,file=filename,action='write',status='replace')
>
>     do angle_deg=-180,180,1
>
>         x=angle_deg*0.0174533    !converting degree to radian
>
>         fx=a0-a1*cos(x)+a2*(cos(x))**2-a3*(cos(x))**3+a4*(cos(x))**4 &
>         -a5*(cos(x))**5
>
>         dfx=sin(x)*(a1-2*a2*cos(x)+3*a3*(cos(x))**2-4*a4*(cos(x))**3+ &
>         5*a5*(cos(x))**4)     !analytical differentiation of
> Ryckaert-Bellemans function
>
>         write(100,*)angle_deg,fx,-dfx
>     end do
> end program table
>
> I used force constant equal to 1 in topology file.
> In npt equlibration, my simulation crashed with lot of LINCS error.
> Would somebody help me figure out where i did the mistake.
>
> Regards
> Masrul
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>